From 17cbf47dd63dd828dba24da58797f47a59906041 Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Wed, 8 Jan 2025 17:56:40 +0000
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---
 _modules/index.html                       |   5 +-
 _modules/singler/aggregate_reference.html | 421 ++++++++++++++++++++++
 _modules/singler/annotate_integrated.html |  20 +-
 _modules/singler/annotate_single.html     |  18 +-
 _modules/singler/classify_integrated.html |  23 +-
 _modules/singler/classify_single.html     |  19 +-
 _modules/singler/get_classic_markers.html |  22 +-
 _modules/singler/train_integrated.html    |  28 +-
 _modules/singler/train_single.html        | 129 +++++--
 _sources/api/singler.rst.txt              |   8 +
 _static/pygments.css                      | 378 +++++++++----------
 api/modules.html                          |   6 +-
 api/singler.html                          | 113 ++++--
 authors.html                              |   2 +-
 changelog.html                            |  11 +-
 contributing.html                         |   2 +-
 genindex.html                             |  15 +-
 index.html                                |   3 +-
 license.html                              |   2 +-
 objects.inv                               | Bin 582 -> 602 bytes
 py-modindex.html                          |   8 +-
 readme.html                               |  14 +-
 search.html                               |   2 +-
 searchindex.js                            |   2 +-
 24 files changed, 908 insertions(+), 343 deletions(-)
 create mode 100644 _modules/singler/aggregate_reference.html
diff --git a/_modules/index.html b/_modules/index.html
index 5d151f2..ccb64d4 100644
--- a/_modules/index.html
+++ b/_modules/index.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Overview: module code - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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@@ -242,7 +242,8 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>All modules for which code is available</h1>
-<ul><li><a href="singler/annotate_integrated.html">singler.annotate_integrated</a></li>
+<ul><li><a href="singler/aggregate_reference.html">singler.aggregate_reference</a></li>
+<li><a href="singler/annotate_integrated.html">singler.annotate_integrated</a></li>
 <li><a href="singler/annotate_single.html">singler.annotate_single</a></li>
 <li><a href="singler/classify_integrated.html">singler.classify_integrated</a></li>
 <li><a href="singler/classify_single.html">singler.classify_single</a></li>
diff --git a/_modules/singler/aggregate_reference.html b/_modules/singler/aggregate_reference.html
new file mode 100644
index 0000000..fb8be3a
--- /dev/null
+++ b/_modules/singler/aggregate_reference.html
@@ -0,0 +1,421 @@
+<!doctype html>
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+        <article role="main" id="furo-main-content">
+          <h1>Source code for singler.aggregate_reference</h1><div class="highlight"><pre>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Union</span>
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">delayedarray</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">summarizedexperiment</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocframe</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">._utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">_clean_matrix</span>
+
+
+<div class="viewcode-block" id="aggregate_reference">
+<a class="viewcode-back" href="../../api/singler.html#singler.aggregate_reference.aggregate_reference">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">aggregate_reference</span><span class="p">(</span>
+    <span class="n">ref_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
+    <span class="n">ref_labels</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
+    <span class="n">ref_features</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
+    <span class="n">num_centers</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">power</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.5</span><span class="p">,</span>
+    <span class="n">num_top</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1000</span><span class="p">,</span>
+    <span class="n">rank</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">20</span><span class="p">,</span>
+    <span class="n">assay_type</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;logcounts&quot;</span><span class="p">,</span>
+    <span class="n">subset_row</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Sequence</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">check_missing</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="n">num_threads</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">summarizedexperiment</span><span class="o">.</span><span class="n">SummarizedExperiment</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Aggregate reference samples for a given label by using vector quantization to average their count profiles.</span>
+<span class="sd">    The idea is to reduce the size of single-cell reference datasets so as to reduce the computation time of :py:func:`~singler.train_single.train_single`.</span>
+<span class="sd">    We perform k-means clustering for all cells in each label and aggregate all cells within each k-means cluster.</span>
+<span class="sd">    (More specifically, the clustering is done on the principal components generated from the highly variable genes to better capture the structure within each label.)</span>
+<span class="sd">    This yields one or more profiles per label, reducing the number of separate observations while preserving some level of intra-label heterogeneity.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        ref_data:</span>
+<span class="sd">            Floating-point matrix of reference expression values, usually containing log-expression values.</span>
+<span class="sd">            Alternatively, a :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment` object containing such a matrix.</span>
+
+<span class="sd">        ref_labels:</span>
+<span class="sd">            Array of length equal to the number of columns in ``ref_data``, containing the labels for each cell.</span>
+
+<span class="sd">        ref_features:</span>
+<span class="sd">            Sequence of identifiers for each feature, i.e., row in ``ref_data``.</span>
+
+<span class="sd">        num_centers:</span>
+<span class="sd">            Maximum number of aggregated profiles to produce for each label with :py:func:`~scranpy.cluster_kmeans.cluster_kmeans`.</span>
+<span class="sd">            If ``None``, a suitable number of profiles is automatically chosen. </span>
+
+<span class="sd">        power:</span>
+<span class="sd">            Number between 0 and 1 indicating how much aggregation should be performed.</span>
+<span class="sd">            Specifically, we set the number of clusters to ``X**power`` where ``X`` is the number of cells assigned to that label.</span>
+<span class="sd">            Ignored if ``num_centers`` is not ``None``.</span>
+
+<span class="sd">        num_top:</span>
+<span class="sd">            Number of highly variable genes to use for PCA prior to clustering, see :py:func:`~scranpy.choose_highly_variable_genes.choose_highly_variable_genes`.</span>
+
+<span class="sd">        rank:</span>
+<span class="sd">            Number of principal components to use during clustering, see :py:func:`~scranpy.run_pca.run_pca`.</span>
+
+<span class="sd">        assay_type:</span>
+<span class="sd">            Integer or string specifying the assay of ``ref_data`` containing the relevant expression matrix,</span>
+<span class="sd">            if ``ref`` is a :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment` object.</span>
+
+<span class="sd">        subset_row:</span>
+<span class="sd">            Array of row indices specifying the rows of ``ref_data`` to use for clustering.</span>
+<span class="sd">            If ``None``, no additional filtering is performed.</span>
+<span class="sd">            Note that even if ``subset_row`` is provided, aggregation is still performed on all genes.</span>
+
+<span class="sd">        check_missing:</span>
+<span class="sd">            Whether to check for and remove rows with missing (NaN) values from ``ref_data``.</span>
+
+<span class="sd">        num_threads:</span>
+<span class="sd">            Number of threads to use.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment` containing the aggregated values in its first assay.</span>
+<span class="sd">        The label for each aggregated profile is stored in the column data.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_features</span> <span class="o">=</span> <span class="n">_clean_matrix</span><span class="p">(</span>
+        <span class="n">ref_data</span><span class="p">,</span>
+        <span class="n">ref_features</span><span class="p">,</span>
+        <span class="n">assay_type</span><span class="o">=</span><span class="n">assay_type</span><span class="p">,</span>
+        <span class="n">check_missing</span><span class="o">=</span><span class="n">check_missing</span><span class="p">,</span>
+        <span class="n">num_threads</span><span class="o">=</span><span class="n">num_threads</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">by_label</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">lab</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">ref_labels</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">lab</span> <span class="ow">in</span> <span class="n">by_label</span><span class="p">:</span>
+            <span class="n">by_label</span><span class="p">[</span><span class="n">lab</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">by_label</span><span class="p">[</span><span class="n">lab</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="p">]</span>
+
+    <span class="n">output_vals</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">output_labels</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">output_names</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="k">for</span> <span class="n">lab</span><span class="p">,</span> <span class="n">chosen</span> <span class="ow">in</span> <span class="n">by_label</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+        <span class="n">current</span> <span class="o">=</span> <span class="n">ref_data</span><span class="p">[:,</span><span class="n">chosen</span><span class="p">]</span>
+
+        <span class="n">cur_num_centers</span> <span class="o">=</span> <span class="n">num_centers</span>
+        <span class="k">if</span> <span class="n">cur_num_centers</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">cur_num_centers</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">current</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">**</span><span class="n">power</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">cur_num_centers</span> <span class="o">&lt;=</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="n">output</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">current</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">),</span> <span class="p">(</span><span class="n">current</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="mi">1</span><span class="p">))</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">subcurrent</span> <span class="o">=</span> <span class="n">current</span>
+            <span class="k">if</span> <span class="n">subset_row</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">subcurrent</span> <span class="o">=</span> <span class="n">subcurrent</span><span class="p">[</span><span class="n">subset_row</span><span class="p">,:]</span>
+
+            <span class="c1"># Doing a mini-analysis here: PCA on HVGs followed by k-means.</span>
+            <span class="kn">import</span><span class="w"> </span><span class="nn">scranpy</span>
+            <span class="n">stats</span> <span class="o">=</span> <span class="n">scranpy</span><span class="o">.</span><span class="n">model_gene_variances</span><span class="p">(</span><span class="n">subcurrent</span><span class="p">,</span> <span class="n">num_threads</span><span class="o">=</span><span class="n">num_threads</span><span class="p">)</span>
+            <span class="n">keep</span> <span class="o">=</span> <span class="n">scranpy</span><span class="o">.</span><span class="n">choose_highly_variable_genes</span><span class="p">(</span><span class="n">stats</span><span class="o">.</span><span class="n">residual</span><span class="p">,</span> <span class="n">top</span><span class="o">=</span><span class="n">num_top</span><span class="p">)</span>
+            <span class="n">subcurrent</span> <span class="o">=</span> <span class="n">subcurrent</span><span class="p">[</span><span class="n">keep</span><span class="p">,:]</span>
+
+            <span class="k">if</span> <span class="n">rank</span> <span class="o">&lt;=</span> <span class="nb">min</span><span class="p">(</span><span class="n">subcurrent</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
+                <span class="n">pcs</span> <span class="o">=</span> <span class="n">scranpy</span><span class="o">.</span><span class="n">run_pca</span><span class="p">(</span><span class="n">subcurrent</span><span class="p">,</span> <span class="n">number</span><span class="o">=</span><span class="n">rank</span><span class="p">,</span> <span class="n">num_threads</span><span class="o">=</span><span class="n">num_threads</span><span class="p">)</span><span class="o">.</span><span class="n">components</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">pcs</span> <span class="o">=</span> <span class="n">subcurrent</span>
+
+            <span class="n">clustered</span> <span class="o">=</span> <span class="n">scranpy</span><span class="o">.</span><span class="n">cluster_kmeans</span><span class="p">(</span><span class="n">pcs</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="n">cur_num_centers</span><span class="p">,</span> <span class="n">num_threads</span><span class="o">=</span><span class="n">num_threads</span><span class="p">)</span>
+            <span class="n">agg</span> <span class="o">=</span> <span class="n">scranpy</span><span class="o">.</span><span class="n">aggregate_across_cells</span><span class="p">(</span><span class="n">current</span><span class="p">,</span> <span class="p">[</span><span class="n">clustered</span><span class="o">.</span><span class="n">clusters</span><span class="p">],</span> <span class="n">num_threads</span><span class="o">=</span><span class="n">num_threads</span><span class="p">)</span>
+            <span class="n">output</span> <span class="o">=</span> <span class="n">agg</span><span class="o">.</span><span class="n">sum</span> <span class="o">/</span> <span class="n">agg</span><span class="o">.</span><span class="n">counts</span>
+
+        <span class="n">output_vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>
+        <span class="n">output_labels</span> <span class="o">+=</span> <span class="p">[</span><span class="n">lab</span><span class="p">]</span> <span class="o">*</span> <span class="n">output</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
+            <span class="n">output_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">lab</span> <span class="o">+</span> <span class="s2">&quot;_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">output_vals</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">output_vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">ref_data</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="mi">0</span><span class="p">)))</span>
+
+    <span class="n">output</span> <span class="o">=</span> <span class="n">summarizedexperiment</span><span class="o">.</span><span class="n">SummarizedExperiment</span><span class="p">(</span>
+        <span class="p">{</span> <span class="s2">&quot;logcounts&quot;</span><span class="p">:</span> <span class="n">numpy</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">output_vals</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="p">},</span>
+        <span class="n">column_data</span> <span class="o">=</span> <span class="n">biocframe</span><span class="o">.</span><span class="n">BiocFrame</span><span class="p">({</span> <span class="s2">&quot;label&quot;</span><span class="p">:</span> <span class="n">output_labels</span> <span class="p">})</span>
+    <span class="p">)</span>
+    <span class="n">output</span><span class="o">.</span><span class="n">set_column_names</span><span class="p">(</span><span class="n">output_names</span><span class="p">,</span> <span class="n">in_place</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">output</span><span class="o">.</span><span class="n">set_row_names</span><span class="p">(</span><span class="n">ref_features</span><span class="p">,</span> <span class="n">in_place</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">output</span></div>
+
+</pre></div>
+        </article>
+      </div>
+      <footer>
+        
+        <div class="related-pages">
+          
+          
+        </div>
+        <div class="bottom-of-page">
+          <div class="left-details">
+            <div class="copyright">
+                Copyright &#169; 2023, Aaron Lun
+            </div>
+            Made with <a href="https://www.sphinx-doc.org/">Sphinx</a> and <a class="muted-link" href="https://pradyunsg.me">@pradyunsg</a>'s
+            
+            <a href="https://github.com/pradyunsg/furo">Furo</a>
+            
+          </div>
+          <div class="right-details">
+            
+          </div>
+        </div>
+        
+      </footer>
+    </div>
+    <aside class="toc-drawer no-toc">
+      
+      
+      
+    </aside>
+  </div>
+</div><script src="../../_static/documentation_options.js?v=3f1b9271"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
+    <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../../_static/scripts/furo.js?v=5fa4622c"></script>
+    </body>
+</html>
\ No newline at end of file
diff --git a/_modules/singler/annotate_integrated.html b/_modules/singler/annotate_integrated.html
index c30aad2..2478af1 100644
--- a/_modules/singler/annotate_integrated.html
+++ b/_modules/singler/annotate_integrated.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler.annotate_integrated - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -242,21 +242,21 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for singler.annotate_integrated</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Union</span>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Union</span>
 
-<span class="kn">import</span> <span class="nn">biocframe</span>
-<span class="kn">import</span> <span class="nn">warnings</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocframe</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
 
-<span class="kn">from</span> <span class="nn">._utils</span> <span class="kn">import</span> <span class="n">_clean_matrix</span><span class="p">,</span> <span class="n">_restrict_features</span>
-<span class="kn">from</span> <span class="nn">.train_single</span> <span class="kn">import</span> <span class="n">train_single</span>
-<span class="kn">from</span> <span class="nn">.train_integrated</span> <span class="kn">import</span> <span class="n">train_integrated</span>
-<span class="kn">from</span> <span class="nn">.classify_single</span> <span class="kn">import</span> <span class="n">classify_single</span>
-<span class="kn">from</span> <span class="nn">.classify_integrated</span> <span class="kn">import</span> <span class="n">classify_integrated</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">._utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">_clean_matrix</span><span class="p">,</span> <span class="n">_restrict_features</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.train_single</span><span class="w"> </span><span class="kn">import</span> <span class="n">train_single</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.train_integrated</span><span class="w"> </span><span class="kn">import</span> <span class="n">train_integrated</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.classify_single</span><span class="w"> </span><span class="kn">import</span> <span class="n">classify_single</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.classify_integrated</span><span class="w"> </span><span class="kn">import</span> <span class="n">classify_integrated</span>
 
 
 <div class="viewcode-block" id="annotate_integrated">
 <a class="viewcode-back" href="../../api/singler.html#singler.annotate_integrated.annotate_integrated">[docs]</a>
-<span class="k">def</span> <span class="nf">annotate_integrated</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">annotate_integrated</span><span class="p">(</span>
     <span class="n">test_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
     <span class="n">ref_data</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
     <span class="n">ref_labels</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">Sequence</span><span class="p">],</span>
diff --git a/_modules/singler/annotate_single.html b/_modules/singler/annotate_single.html
index d6f4c2e..de8893c 100644
--- a/_modules/singler/annotate_single.html
+++ b/_modules/singler/annotate_single.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler.annotate_single - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -242,20 +242,20 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for singler.annotate_single</h1><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">warnings</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
 
-<span class="kn">import</span> <span class="nn">biocframe</span>
-<span class="kn">import</span> <span class="nn">summarizedexperiment</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocframe</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">summarizedexperiment</span>
 
-<span class="kn">from</span> <span class="nn">.train_single</span> <span class="kn">import</span> <span class="n">train_single</span> 
-<span class="kn">from</span> <span class="nn">.classify_single</span> <span class="kn">import</span> <span class="n">classify_single</span>
-<span class="kn">from</span> <span class="nn">._utils</span> <span class="kn">import</span> <span class="n">_clean_matrix</span><span class="p">,</span> <span class="n">_restrict_features</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.train_single</span><span class="w"> </span><span class="kn">import</span> <span class="n">train_single</span> 
+<span class="kn">from</span><span class="w"> </span><span class="nn">.classify_single</span><span class="w"> </span><span class="kn">import</span> <span class="n">classify_single</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">._utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">_clean_matrix</span><span class="p">,</span> <span class="n">_restrict_features</span>
 
 
 <div class="viewcode-block" id="annotate_single">
 <a class="viewcode-back" href="../../api/singler.html#singler.annotate_single.annotate_single">[docs]</a>
-<span class="k">def</span> <span class="nf">annotate_single</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">annotate_single</span><span class="p">(</span>
     <span class="n">test_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
     <span class="n">ref_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
     <span class="n">ref_labels</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
diff --git a/_modules/singler/classify_integrated.html b/_modules/singler/classify_integrated.html
index 870ba9f..ea26825 100644
--- a/_modules/singler/classify_integrated.html
+++ b/_modules/singler/classify_integrated.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler.classify_integrated - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -242,21 +242,21 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for singler.classify_integrated</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
 
-<span class="kn">import</span> <span class="nn">biocutils</span>
-<span class="kn">import</span> <span class="nn">biocframe</span> 
-<span class="kn">import</span> <span class="nn">mattress</span>
-<span class="kn">import</span> <span class="nn">summarizedexperiment</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocutils</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocframe</span> 
+<span class="kn">import</span><span class="w"> </span><span class="nn">mattress</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">summarizedexperiment</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span>
 
-<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
-<span class="kn">from</span> <span class="nn">.train_integrated</span> <span class="kn">import</span> <span class="n">TrainedIntegratedReferences</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.train_integrated</span><span class="w"> </span><span class="kn">import</span> <span class="n">TrainedIntegratedReferences</span>
 
 
 <div class="viewcode-block" id="classify_integrated">
 <a class="viewcode-back" href="../../api/singler.html#singler.classify_integrated.classify_integrated">[docs]</a>
-<span class="k">def</span> <span class="nf">classify_integrated</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">classify_integrated</span><span class="p">(</span>
     <span class="n">test_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
     <span class="n">results</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">biocframe</span><span class="o">.</span><span class="n">BiocFrame</span><span class="p">],</span>
     <span class="n">integrated_prebuilt</span><span class="p">:</span> <span class="n">TrainedIntegratedReferences</span><span class="p">,</span>
@@ -323,9 +323,6 @@ <h1>Source code for singler.classify_integrated</h1><div class="highlight"><pre>
     <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">test_data</span><span class="p">,</span> <span class="n">summarizedexperiment</span><span class="o">.</span><span class="n">SummarizedExperiment</span><span class="p">):</span>
         <span class="n">test_data</span> <span class="o">=</span> <span class="n">test_data</span><span class="o">.</span><span class="n">assay</span><span class="p">(</span><span class="n">assay_type</span><span class="p">)</span>
 
-    <span class="k">if</span> <span class="n">test_data</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="n">integrated_prebuilt</span><span class="o">.</span><span class="n">_test_num_features</span><span class="p">:</span> <span class="c1"># TODO: move to singlepp.</span>
-        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;number of rows in &#39;test_data&#39; is not consistent with &#39;test_features=&#39; used to create &#39;integrated_prebuilt&#39;&quot;</span><span class="p">)</span>
-
     <span class="n">ref_labs</span> <span class="o">=</span> <span class="n">integrated_prebuilt</span><span class="o">.</span><span class="n">reference_labels</span>
     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">results</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ref_labs</span><span class="p">):</span>
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;length of &#39;results&#39; should equal the number of references&quot;</span><span class="p">)</span>
diff --git a/_modules/singler/classify_single.html b/_modules/singler/classify_single.html
index cce44d8..b5f268e 100644
--- a/_modules/singler/classify_single.html
+++ b/_modules/singler/classify_single.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler.classify_single - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -242,19 +242,19 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for singler.classify_single</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
 
-<span class="kn">import</span> <span class="nn">biocframe</span>
-<span class="kn">import</span> <span class="nn">mattress</span>
-<span class="kn">import</span> <span class="nn">summarizedexperiment</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocframe</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">mattress</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">summarizedexperiment</span>
 
-<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
-<span class="kn">from</span> <span class="nn">.train_single</span> <span class="kn">import</span> <span class="n">TrainedSingleReference</span> 
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.train_single</span><span class="w"> </span><span class="kn">import</span> <span class="n">TrainedSingleReference</span> 
 
 
 <div class="viewcode-block" id="classify_single">
 <a class="viewcode-back" href="../../api/singler.html#singler.classify_single.classify_single">[docs]</a>
-<span class="k">def</span> <span class="nf">classify_single</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">classify_single</span><span class="p">(</span>
     <span class="n">test_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
     <span class="n">ref_prebuilt</span><span class="p">:</span> <span class="n">TrainedSingleReference</span><span class="p">,</span>
     <span class="n">assay_type</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
@@ -312,9 +312,6 @@ <h1>Source code for singler.classify_single</h1><div class="highlight"><pre>
     <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">test_data</span><span class="p">,</span> <span class="n">summarizedexperiment</span><span class="o">.</span><span class="n">SummarizedExperiment</span><span class="p">):</span>
         <span class="n">test_data</span> <span class="o">=</span> <span class="n">test_data</span><span class="o">.</span><span class="n">assay</span><span class="p">(</span><span class="n">assay_type</span><span class="p">)</span>
 
-    <span class="k">if</span> <span class="n">test_data</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="n">ref_prebuilt</span><span class="o">.</span><span class="n">_test_num_features</span><span class="p">:</span> <span class="c1"># TODO: move to singlepp</span>
-        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;number of rows in &#39;test_data&#39; is not consistent with &#39;test_features=&#39; used to create &#39;ref_prebuilt&#39;&quot;</span><span class="p">)</span>
-
     <span class="n">test_ptr</span> <span class="o">=</span> <span class="n">mattress</span><span class="o">.</span><span class="n">initialize</span><span class="p">(</span><span class="n">test_data</span><span class="p">)</span>
 
     <span class="n">best</span><span class="p">,</span> <span class="n">raw_scores</span><span class="p">,</span> <span class="n">delta</span> <span class="o">=</span> <span class="n">lib</span><span class="o">.</span><span class="n">classify_single</span><span class="p">(</span>
diff --git a/_modules/singler/get_classic_markers.html b/_modules/singler/get_classic_markers.html
index 45e72b2..7aa8cb1 100644
--- a/_modules/singler/get_classic_markers.html
+++ b/_modules/singler/get_classic_markers.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler.get_classic_markers - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -242,15 +242,15 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for singler.get_classic_markers</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
 
-<span class="kn">import</span> <span class="nn">delayedarray</span>
-<span class="kn">import</span> <span class="nn">mattress</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
-<span class="kn">import</span> <span class="nn">biocutils</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">delayedarray</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">mattress</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocutils</span>
 
-<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
-<span class="kn">from</span> <span class="nn">._utils</span> <span class="kn">import</span> <span class="p">(</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">._utils</span><span class="w"> </span><span class="kn">import</span> <span class="p">(</span>
     <span class="n">_clean_matrix</span><span class="p">,</span>
     <span class="n">_create_map</span><span class="p">,</span>
     <span class="n">_stable_intersect</span><span class="p">,</span>
@@ -258,7 +258,7 @@ <h1>Source code for singler.get_classic_markers</h1><div class="highlight"><pre>
 <span class="p">)</span>
 
 
-<span class="k">def</span> <span class="nf">_get_classic_markers_raw</span><span class="p">(</span><span class="n">ref_ptrs</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">ref_labels</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">num_de</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">num_threads</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_get_classic_markers_raw</span><span class="p">(</span><span class="n">ref_ptrs</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">ref_labels</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">num_de</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">num_threads</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
     <span class="n">nrefs</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ref_ptrs</span><span class="p">)</span>
 
     <span class="c1"># We assume that ref_ptrs and ref_features contains the outputs of</span>
@@ -334,7 +334,7 @@ <h1>Source code for singler.get_classic_markers</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="get_classic_markers">
 <a class="viewcode-back" href="../../api/singler.html#singler.get_classic_markers.get_classic_markers">[docs]</a>
-<span class="k">def</span> <span class="nf">get_classic_markers</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">get_classic_markers</span><span class="p">(</span>
     <span class="n">ref_data</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">list</span><span class="p">[</span><span class="n">Any</span><span class="p">]],</span>
     <span class="n">ref_labels</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">Sequence</span><span class="p">,</span> <span class="nb">list</span><span class="p">[</span><span class="n">Sequence</span><span class="p">]],</span>
     <span class="n">ref_features</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">Sequence</span><span class="p">,</span> <span class="nb">list</span><span class="p">[</span><span class="n">Sequence</span><span class="p">]],</span>
@@ -446,7 +446,7 @@ <h1>Source code for singler.get_classic_markers</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="number_of_classic_markers">
 <a class="viewcode-back" href="../../api/singler.html#singler.get_classic_markers.number_of_classic_markers">[docs]</a>
-<span class="k">def</span> <span class="nf">number_of_classic_markers</span><span class="p">(</span><span class="n">num_labels</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">number_of_classic_markers</span><span class="p">(</span><span class="n">num_labels</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Compute the number of markers to detect for a given number of labels,</span>
 <span class="sd">    using the classic SingleR marker detection algorithm.</span>
 
diff --git a/_modules/singler/train_integrated.html b/_modules/singler/train_integrated.html
index 5673ab7..a5eb3e5 100644
--- a/_modules/singler/train_integrated.html
+++ b/_modules/singler/train_integrated.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler.train_integrated - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -242,31 +242,30 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for singler.train_integrated</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Union</span>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Union</span>
 
-<span class="kn">import</span> <span class="nn">numpy</span> 
-<span class="kn">import</span> <span class="nn">biocutils</span>
-<span class="kn">import</span> <span class="nn">warnings</span>
-<span class="kn">import</span> <span class="nn">mattress</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span> 
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocutils</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">mattress</span>
 
-<span class="kn">from</span> <span class="nn">.train_single</span> <span class="kn">import</span> <span class="n">TrainedSingleReference</span>
-<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
-<span class="kn">from</span> <span class="nn">._utils</span> <span class="kn">import</span> <span class="n">_stable_union</span><span class="p">,</span> <span class="n">_stable_intersect</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.train_single</span><span class="w"> </span><span class="kn">import</span> <span class="n">TrainedSingleReference</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">._utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">_stable_union</span><span class="p">,</span> <span class="n">_stable_intersect</span>
 
 
 <div class="viewcode-block" id="TrainedIntegratedReferences">
 <a class="viewcode-back" href="../../api/singler.html#singler.train_integrated.TrainedIntegratedReferences">[docs]</a>
-<span class="k">class</span> <span class="nc">TrainedIntegratedReferences</span><span class="p">:</span>
+<span class="k">class</span><span class="w"> </span><span class="nc">TrainedIntegratedReferences</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Object containing integrated references, typically constructed by</span>
 <span class="sd">    :py:meth:`~singler.train_integrated.train_integrated`.&quot;&quot;&quot;</span>
 
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ptr</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">ref_labels</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">test_num_features</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
+    <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ptr</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">ref_labels</span><span class="p">:</span> <span class="nb">list</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_ptr</span> <span class="o">=</span> <span class="n">ptr</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_labels</span> <span class="o">=</span> <span class="n">ref_labels</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_test_num_features</span> <span class="o">=</span> <span class="n">test_num_features</span> <span class="c1"># TODO: move to singlepp.</span>
 
     <span class="nd">@property</span>
-    <span class="k">def</span> <span class="nf">reference_labels</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">reference_labels</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;List of lists containing the names of the labels for each reference.</span>
 
 <span class="sd">        Each entry corresponds to a reference in :py:attr:`~reference_names`,</span>
@@ -278,7 +277,7 @@ <h1>Source code for singler.train_integrated</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="train_integrated">
 <a class="viewcode-back" href="../../api/singler.html#singler.train_integrated.train_integrated">[docs]</a>
-<span class="k">def</span> <span class="nf">train_integrated</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">train_integrated</span><span class="p">(</span>
     <span class="n">test_features</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
     <span class="n">ref_prebuilt</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">TrainedSingleReference</span><span class="p">],</span>
     <span class="n">warn_lost</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
@@ -336,7 +335,6 @@ <h1>Source code for singler.train_integrated</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">TrainedIntegratedReferences</span><span class="p">(</span>
         <span class="n">ptr</span><span class="o">=</span><span class="n">ibuilt</span><span class="p">,</span>
         <span class="n">ref_labels</span><span class="o">=</span><span class="p">[</span><span class="n">x</span><span class="o">.</span><span class="n">labels</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">ref_prebuilt</span><span class="p">],</span>
-        <span class="n">test_num_features</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">test_features</span><span class="p">),</span>
     <span class="p">)</span></div>
 
 </pre></div>
diff --git a/_modules/singler/train_single.html b/_modules/singler/train_single.html
index 5583610..92060a4 100644
--- a/_modules/singler/train_single.html
+++ b/_modules/singler/train_single.html
@@ -6,7 +6,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler.train_single - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -242,29 +242,30 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
 
-<span class="kn">import</span> <span class="nn">biocutils</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
-<span class="kn">import</span> <span class="nn">knncolle</span>
-<span class="kn">import</span> <span class="nn">mattress</span>
-<span class="kn">import</span> <span class="nn">delayedarray</span>
-<span class="kn">import</span> <span class="nn">warnings</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">biocutils</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">knncolle</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">mattress</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">delayedarray</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
 
-<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
-<span class="kn">from</span> <span class="nn">._utils</span> <span class="kn">import</span> <span class="n">_clean_matrix</span><span class="p">,</span> <span class="n">_restrict_features</span><span class="p">,</span> <span class="n">_stable_intersect</span>
-<span class="kn">from</span> <span class="nn">.get_classic_markers</span> <span class="kn">import</span> <span class="n">get_classic_markers</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">lib_singler</span> <span class="k">as</span> <span class="n">lib</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">._utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">_clean_matrix</span><span class="p">,</span> <span class="n">_restrict_features</span><span class="p">,</span> <span class="n">_stable_intersect</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.get_classic_markers</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_classic_markers</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.aggregate_reference</span><span class="w"> </span><span class="kn">import</span> <span class="n">aggregate_reference</span>
 
 
 <div class="viewcode-block" id="TrainedSingleReference">
 <a class="viewcode-back" href="../../api/singler.html#singler.train_single.TrainedSingleReference">[docs]</a>
-<span class="k">class</span> <span class="nc">TrainedSingleReference</span><span class="p">:</span>
+<span class="k">class</span><span class="w"> </span><span class="nc">TrainedSingleReference</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;A prebuilt reference object, typically created by</span>
 <span class="sd">    :py:meth:`~singler.train_single.train_single`. This is intended for</span>
 <span class="sd">    advanced users only and should not be serialized.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">ptr</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
         <span class="n">full_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
@@ -272,7 +273,6 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
         <span class="n">labels</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
         <span class="n">features</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
         <span class="n">markers</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">]],</span>
-        <span class="n">test_num_features</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
     <span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_ptr</span> <span class="o">=</span> <span class="n">ptr</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_full_data</span> <span class="o">=</span> <span class="n">full_data</span>
@@ -280,11 +280,10 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_features</span> <span class="o">=</span> <span class="n">features</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_labels</span> <span class="o">=</span> <span class="n">labels</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_markers</span> <span class="o">=</span> <span class="n">markers</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_test_num_features</span> <span class="o">=</span> <span class="n">test_num_features</span> <span class="c1"># TODO: move to singlepp.</span>
 
 <div class="viewcode-block" id="TrainedSingleReference.num_markers">
 <a class="viewcode-back" href="../../api/singler.html#singler.train_single.TrainedSingleReference.num_markers">[docs]</a>
-    <span class="k">def</span> <span class="nf">num_markers</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">num_markers</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Returns:</span>
 <span class="sd">            Number of markers to be used for classification. This is the</span>
@@ -295,7 +294,7 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="TrainedSingleReference.num_labels">
 <a class="viewcode-back" href="../../api/singler.html#singler.train_single.TrainedSingleReference.num_labels">[docs]</a>
-    <span class="k">def</span> <span class="nf">num_labels</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">num_labels</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Returns:</span>
 <span class="sd">            Number of unique labels in this reference.</span>
@@ -304,23 +303,23 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
 
 
     <span class="nd">@property</span>
-    <span class="k">def</span> <span class="nf">features</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">features</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;The universe of features known to this reference.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_features</span>
 
     <span class="nd">@property</span>
-    <span class="k">def</span> <span class="nf">labels</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Sequence</span><span class="p">:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">labels</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Sequence</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Unique labels in this reference.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_labels</span>
 
     <span class="nd">@property</span>
-    <span class="k">def</span> <span class="nf">markers</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">list</span><span class="p">]]:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">markers</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">list</span><span class="p">]]:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Markers for every pairwise comparison between labels.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_markers</span>
 
 <div class="viewcode-block" id="TrainedSingleReference.marker_subset">
 <a class="viewcode-back" href="../../api/singler.html#singler.train_single.TrainedSingleReference.marker_subset">[docs]</a>
-    <span class="k">def</span> <span class="nf">marker_subset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">indices_only</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="n">numpy</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="nb">list</span><span class="p">]:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">marker_subset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">indices_only</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="n">numpy</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="nb">list</span><span class="p">]:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Args:</span>
 <span class="sd">            indices_only:</span>
@@ -342,7 +341,7 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
 
 
 
-<span class="k">def</span> <span class="nf">_markers_from_dict</span><span class="p">(</span><span class="n">markers</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">]],</span> <span class="n">labels</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">available_features</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_markers_from_dict</span><span class="p">(</span><span class="n">markers</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">]],</span> <span class="n">labels</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">available_features</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">):</span>
     <span class="n">fmapping</span> <span class="o">=</span> <span class="p">{}</span>
     <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">available_features</span><span class="p">):</span>
         <span class="n">fmapping</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="o">=</span> <span class="n">i</span>
@@ -351,7 +350,7 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="train_single">
 <a class="viewcode-back" href="../../api/singler.html#singler.train_single.train_single">[docs]</a>
-<span class="k">def</span> <span class="nf">train_single</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">train_single</span><span class="p">(</span>
     <span class="n">ref_data</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
     <span class="n">ref_labels</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
     <span class="n">ref_features</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">,</span>
@@ -360,8 +359,11 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
     <span class="n">restrict_to</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">set</span><span class="p">,</span> <span class="nb">dict</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="n">check_missing</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
     <span class="n">markers</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">]]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-    <span class="n">marker_method</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;classic&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;classic&quot;</span><span class="p">,</span>
+    <span class="n">marker_method</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;classic&quot;</span><span class="p">,</span> <span class="s2">&quot;auc&quot;</span><span class="p">,</span> <span class="s2">&quot;cohens_d&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;classic&quot;</span><span class="p">,</span>
+    <span class="n">num_de</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="n">marker_args</span><span class="p">:</span> <span class="nb">dict</span> <span class="o">=</span> <span class="p">{},</span>
+    <span class="n">aggregate</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="n">aggregate_args</span><span class="p">:</span> <span class="nb">dict</span> <span class="o">=</span> <span class="p">{},</span>
     <span class="n">nn_parameters</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">knncolle</span><span class="o">.</span><span class="n">Parameters</span><span class="p">]</span> <span class="o">=</span> <span class="n">knncolle</span><span class="o">.</span><span class="n">VptreeParameters</span><span class="p">(),</span>
     <span class="n">num_threads</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">TrainedSingleReference</span><span class="p">:</span>
@@ -411,15 +413,28 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
 <span class="sd">            should have keys in the inner and outer dictionaries.</span>
 
 <span class="sd">        marker_method:</span>
-<span class="sd">            Method to identify markers from each pairwise comparisons between</span>
-<span class="sd">            labels in ``ref_data``.  If &quot;classic&quot;, we call</span>
-<span class="sd">            :py:meth:`~singler.get_classic_markers.get_classic_markers`.</span>
+<span class="sd">            Method to identify markers from each pairwise comparisons between labels in ``ref_data``.</span>
+<span class="sd">            If ``classic``, we call :py:func:`~singler.get_classic_markers.get_classic_markers`.</span>
+<span class="sd">            If ``auc`` or ``cohens_d``, we call :py:func:`~scranpy.score_markers.score_markers`.</span>
+<span class="sd">            Only used if ``markers`` is not supplied.</span>
+
+<span class="sd">        num_de:</span>
+<span class="sd">            Number of differentially expressed genes to use as markers for each pairwise comparison between labels.</span>
+<span class="sd">            If ``None`` and ``marker_method = &quot;classic&quot;``, an appropriate number of genes is determined by :py:func:`~singler.get_classic_markers.get_classic_markers`.</span>
+<span class="sd">            Otherwise, it is set to 10.</span>
 <span class="sd">            Only used if ``markers`` is not supplied.</span>
 
 <span class="sd">        marker_args:</span>
 <span class="sd">            Further arguments to pass to the chosen marker detection method.</span>
+<span class="sd">            If ``marker_method = &quot;classic&quot;``, this is :py:func:`~singler.get_classic_markers.get_classic_markers`, otherwise it is :py:func:`~scranpy.score_markers.score_markers`.</span>
 <span class="sd">            Only used if ``markers`` is not supplied.</span>
 
+<span class="sd">        aggregate:</span>
+<span class="sd">            Whether the reference dataset should be aggregated to pseudo-bulk samples for speed, see :py:func:`~singler.aggregate_reference.aggregate_reference` for details.</span>
+
+<span class="sd">        aggregate_args:</span>
+<span class="sd">            Further arguments to pass to :py:func:`~singler.aggregate_reference.aggregate_reference` when ``aggregate = True``.</span>
+
 <span class="sd">        nn_parameters:</span>
 <span class="sd">            Algorithm for constructing the neighbor search index, used to</span>
 <span class="sd">            compute scores during classification.</span>
@@ -464,9 +479,7 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
                 <span class="n">keep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
         <span class="n">ref_data</span> <span class="o">=</span> <span class="n">delayedarray</span><span class="o">.</span><span class="n">DelayedArray</span><span class="p">(</span><span class="n">ref_data</span><span class="p">)[:,</span><span class="n">keep</span><span class="p">]</span>
         <span class="n">ref_labels</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">subset_sequence</span><span class="p">(</span><span class="n">ref_labels</span><span class="p">,</span> <span class="n">keep</span><span class="p">)</span>
-    <span class="n">ref_labels</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">Factor</span><span class="o">.</span><span class="n">from_sequence</span><span class="p">(</span><span class="n">ref_labels</span><span class="p">,</span> <span class="n">sort_levels</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> <span class="c1"># TODO: add a dtype= option.</span>
-    <span class="n">unique_labels</span> <span class="o">=</span> <span class="n">ref_labels</span><span class="o">.</span><span class="n">levels</span>
-    <span class="n">label_idx</span> <span class="o">=</span> <span class="n">ref_labels</span><span class="o">.</span><span class="n">codes</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">uint32</span><span class="p">,</span> <span class="n">copy</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+    <span class="n">unique_labels</span><span class="p">,</span> <span class="n">label_idx</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">factorize</span><span class="p">(</span><span class="n">ref_labels</span><span class="p">,</span> <span class="n">sort_levels</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">uint32</span><span class="p">,</span> <span class="n">fail_missing</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
     <span class="n">markers</span> <span class="o">=</span> <span class="n">_identify_genes</span><span class="p">(</span>
         <span class="n">ref_data</span><span class="o">=</span><span class="n">ref_data</span><span class="p">,</span> 
@@ -475,6 +488,7 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
         <span class="n">unique_labels</span><span class="o">=</span><span class="n">unique_labels</span><span class="p">,</span>
         <span class="n">markers</span><span class="o">=</span><span class="n">markers</span><span class="p">,</span>
         <span class="n">marker_method</span><span class="o">=</span><span class="n">marker_method</span><span class="p">,</span>
+        <span class="n">num_de</span><span class="o">=</span><span class="n">num_de</span><span class="p">,</span>
         <span class="n">test_features</span><span class="o">=</span><span class="n">test_features</span><span class="p">,</span>
         <span class="n">restrict_to</span><span class="o">=</span><span class="n">restrict_to</span><span class="p">,</span>
         <span class="n">marker_args</span><span class="o">=</span><span class="n">marker_args</span><span class="p">,</span>
@@ -491,12 +505,15 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
     <span class="k">if</span> <span class="n">test_features</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">test_features_idx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ref_features</span><span class="p">)),</span> <span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">uint32</span><span class="p">)</span>
         <span class="n">ref_features_idx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ref_features</span><span class="p">)),</span> <span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">uint32</span><span class="p">)</span>
-        <span class="n">test_num_features</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ref_features</span><span class="p">)</span>
     <span class="k">else</span><span class="p">:</span>
         <span class="n">common_features</span> <span class="o">=</span> <span class="n">_stable_intersect</span><span class="p">(</span><span class="n">test_features</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">)</span>
         <span class="n">test_features_idx</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">common_features</span><span class="p">,</span> <span class="n">test_features</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">uint32</span><span class="p">)</span>
         <span class="n">ref_features_idx</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">common_features</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">uint32</span><span class="p">)</span>
-        <span class="n">test_num_features</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">test_features</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">aggregate</span><span class="p">:</span>
+        <span class="n">aggr</span> <span class="o">=</span> <span class="n">aggregate_reference</span><span class="p">(</span><span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_labels</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">,</span> <span class="o">**</span><span class="n">aggregate_args</span><span class="p">)</span>
+        <span class="n">ref_data</span> <span class="o">=</span> <span class="n">aggr</span><span class="o">.</span><span class="n">assay</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+        <span class="n">label_idx</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">aggr</span><span class="o">.</span><span class="n">get_column_data</span><span class="p">()</span><span class="o">.</span><span class="n">get_column</span><span class="p">(</span><span class="s2">&quot;label&quot;</span><span class="p">),</span> <span class="n">unique_labels</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">uint32</span><span class="p">)</span>
 
     <span class="n">ref_ptr</span> <span class="o">=</span> <span class="n">mattress</span><span class="o">.</span><span class="n">initialize</span><span class="p">(</span><span class="n">ref_data</span><span class="p">)</span>
     <span class="n">builder</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">knncolle</span><span class="o">.</span><span class="n">define_builder</span><span class="p">(</span><span class="n">nn_parameters</span><span class="p">)</span>
@@ -515,12 +532,11 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
         <span class="n">labels</span> <span class="o">=</span> <span class="n">unique_labels</span><span class="p">,</span>
         <span class="n">features</span> <span class="o">=</span> <span class="n">ref_features</span><span class="p">,</span>
         <span class="n">markers</span> <span class="o">=</span> <span class="n">markers</span><span class="p">,</span>
-        <span class="n">test_num_features</span> <span class="o">=</span> <span class="n">test_num_features</span><span class="p">,</span>
     <span class="p">)</span></div>
 
 
 
-<span class="k">def</span> <span class="nf">_identify_genes</span><span class="p">(</span><span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">,</span> <span class="n">ref_labels</span><span class="p">,</span> <span class="n">unique_labels</span><span class="p">,</span> <span class="n">markers</span><span class="p">,</span> <span class="n">marker_method</span><span class="p">,</span> <span class="n">test_features</span><span class="p">,</span> <span class="n">restrict_to</span><span class="p">,</span> <span class="n">marker_args</span><span class="p">,</span> <span class="n">num_threads</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_identify_genes</span><span class="p">(</span><span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">,</span> <span class="n">ref_labels</span><span class="p">,</span> <span class="n">unique_labels</span><span class="p">,</span> <span class="n">markers</span><span class="p">,</span> <span class="n">marker_method</span><span class="p">,</span> <span class="n">test_features</span><span class="p">,</span> <span class="n">restrict_to</span><span class="p">,</span> <span class="n">num_de</span><span class="p">,</span> <span class="n">marker_args</span><span class="p">,</span> <span class="n">num_threads</span><span class="p">):</span>
     <span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_features</span> <span class="o">=</span> <span class="n">_restrict_features</span><span class="p">(</span><span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">,</span> <span class="n">test_features</span><span class="p">)</span>
     <span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_features</span> <span class="o">=</span> <span class="n">_restrict_features</span><span class="p">(</span><span class="n">ref_data</span><span class="p">,</span> <span class="n">ref_features</span><span class="p">,</span> <span class="n">restrict_to</span><span class="p">)</span>
 
@@ -532,11 +548,52 @@ <h1>Source code for singler.train_single</h1><div class="highlight"><pre>
                 <span class="n">ref_labels</span><span class="o">=</span><span class="p">[</span><span class="n">ref_labels</span><span class="p">],</span>
                 <span class="n">ref_features</span><span class="o">=</span><span class="p">[</span><span class="n">ref_features</span><span class="p">],</span>
                 <span class="n">num_threads</span><span class="o">=</span><span class="n">num_threads</span><span class="p">,</span>
+                <span class="n">num_de</span><span class="o">=</span><span class="n">num_de</span><span class="p">,</span>
                 <span class="o">**</span><span class="n">marker_args</span><span class="p">,</span>
             <span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s2">&quot;other marker methods are not yet implemented, sorry&quot;</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">markers</span>
+            <span class="k">if</span> <span class="n">marker_method</span> <span class="o">==</span> <span class="s2">&quot;auc&quot;</span><span class="p">:</span>
+                <span class="n">compute_auc</span> <span class="o">=</span> <span class="kc">True</span>
+                <span class="n">compute_cohens_d</span> <span class="o">=</span> <span class="kc">False</span> 
+                <span class="n">effect_size</span> <span class="o">=</span> <span class="s2">&quot;auc&quot;</span>
+                <span class="n">boundary</span> <span class="o">=</span> <span class="mf">0.5</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">compute_auc</span> <span class="o">=</span> <span class="kc">False</span> 
+                <span class="n">compute_cohens_d</span> <span class="o">=</span> <span class="kc">True</span>
+                <span class="n">effect_size</span> <span class="o">=</span> <span class="s2">&quot;cohens_d&quot;</span>
+                <span class="n">boundary</span> <span class="o">=</span> <span class="mi">0</span>
+
+            <span class="kn">import</span><span class="w"> </span><span class="nn">scranpy</span>
+            <span class="n">stats</span> <span class="o">=</span> <span class="n">scranpy</span><span class="o">.</span><span class="n">score_markers</span><span class="p">(</span>
+                <span class="n">ref_data</span><span class="p">,</span>
+                <span class="n">groups</span><span class="o">=</span><span class="n">ref_labels</span><span class="p">,</span>
+                <span class="n">num_threads</span><span class="o">=</span><span class="n">num_threads</span><span class="p">,</span>
+                <span class="n">all_pairwise</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+                <span class="n">compute_delta_detected</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+                <span class="n">compute_delta_mean</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+                <span class="n">compute_auc</span><span class="o">=</span><span class="n">compute_auc</span><span class="p">,</span>
+                <span class="n">compute_cohens_d</span><span class="o">=</span><span class="n">compute_cohens_d</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">marker_args</span>
+            <span class="p">)</span>
+            <span class="n">pairwise</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">stats</span><span class="p">,</span> <span class="n">effect_size</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">num_de</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">num_de</span> <span class="o">=</span> <span class="mi">10</span>
+
+            <span class="n">markers</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="k">for</span> <span class="n">g1</span><span class="p">,</span> <span class="n">group1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">stats</span><span class="o">.</span><span class="n">groups</span><span class="p">):</span>
+                <span class="n">group_markers</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="k">for</span> <span class="n">g2</span><span class="p">,</span> <span class="n">group2</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">stats</span><span class="o">.</span><span class="n">groups</span><span class="p">):</span>
+                    <span class="k">if</span> <span class="n">g1</span> <span class="o">==</span> <span class="n">g2</span><span class="p">:</span>
+                        <span class="n">group_markers</span><span class="p">[</span><span class="n">group2</span><span class="p">]</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">StringList</span><span class="p">()</span>
+                        <span class="k">continue</span>
+                    <span class="n">cureffects</span> <span class="o">=</span> <span class="n">pairwise</span><span class="p">[</span><span class="n">g2</span><span class="p">,</span> <span class="n">g1</span><span class="p">,</span> <span class="p">:]</span> <span class="c1"># remember, second dimension is the first group in the comparison.</span>
+                    <span class="n">keep</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">which</span><span class="p">(</span><span class="n">cureffects</span> <span class="o">&gt;</span> <span class="n">boundary</span><span class="p">)</span>
+                    <span class="n">o</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="o">-</span><span class="n">cureffects</span><span class="p">[</span><span class="n">keep</span><span class="p">],</span> <span class="n">stable</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                    <span class="n">group_markers</span><span class="p">[</span><span class="n">group2</span><span class="p">]</span> <span class="o">=</span> <span class="n">biocutils</span><span class="o">.</span><span class="n">StringList</span><span class="p">(</span><span class="n">biocutils</span><span class="o">.</span><span class="n">subset_sequence</span><span class="p">(</span><span class="n">ref_features</span><span class="p">,</span> <span class="n">keep</span><span class="p">[</span><span class="n">o</span><span class="p">[:</span><span class="nb">min</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">o</span><span class="p">),</span> <span class="n">num_de</span><span class="p">)]]))</span>
+                <span class="n">markers</span><span class="p">[</span><span class="n">group1</span><span class="p">]</span> <span class="o">=</span> <span class="n">group_markers</span> 
+
+            <span class="k">return</span> <span class="n">markers</span>
 
     <span class="c1"># Validating a user-supplied list of markers.</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">markers</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
diff --git a/_sources/api/singler.rst.txt b/_sources/api/singler.rst.txt
index 4cc52ca..c9f3798 100644
--- a/_sources/api/singler.rst.txt
+++ b/_sources/api/singler.rst.txt
@@ -9,6 +9,14 @@ singler package
 Submodules
 ----------
 
+singler.aggregate\_reference module
+-----------------------------------
+
+.. automodule:: singler.aggregate_reference
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 singler.annotate\_integrated module
 -----------------------------------
 
diff --git a/_static/pygments.css b/_static/pygments.css
index d0ae3b8..cb16a42 100644
--- a/_static/pygments.css
+++ b/_static/pygments.css
@@ -6,26 +6,26 @@
 .highlight .hll { background-color: #ffffcc }
 .highlight { background: #eeffcc; }
 .highlight .c { color: #408090; font-style: italic } /* Comment */
-.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .err { border: 1px solid #F00 } /* Error */
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-.highlight .o { color: #666666 } /* Operator */
+.highlight .o { color: #666 } /* Operator */
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 .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
 .highlight .cp { color: #007020 } /* Comment.Preproc */
 .highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
 .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
-.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.highlight .cs { color: #408090; background-color: #FFF0F0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
 .highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
-.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gr { color: #F00 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */
-.highlight .go { color: #333333 } /* Generic.Output */
-.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.highlight .go { color: #333 } /* Generic.Output */
+.highlight .gp { color: #C65D09; font-weight: bold } /* Generic.Prompt */
 .highlight .gs { font-weight: bold } /* Generic.Strong */
 .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
-.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .gt { color: #04D } /* Generic.Traceback */
 .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
 .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
 .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
@@ -33,45 +33,45 @@
 .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
 .highlight .kt { color: #902000 } /* Keyword.Type */
 .highlight .m { color: #208050 } /* Literal.Number */
-.highlight .s { color: #4070a0 } /* Literal.String */
-.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .s { color: #4070A0 } /* Literal.String */
+.highlight .na { color: #4070A0 } /* Name.Attribute */
 .highlight .nb { color: #007020 } /* Name.Builtin */
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 .highlight .ne { color: #007020 } /* Name.Exception */
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+.highlight .nf { color: #06287E } /* Name.Function */
 .highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
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+.highlight .nn { color: #0E84B5; font-weight: bold } /* Name.Namespace */
 .highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
-.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .nv { color: #BB60D5 } /* Name.Variable */
 .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
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+.highlight .w { color: #BBB } /* Text.Whitespace */
 .highlight .mb { color: #208050 } /* Literal.Number.Bin */
 .highlight .mf { color: #208050 } /* Literal.Number.Float */
 .highlight .mh { color: #208050 } /* Literal.Number.Hex */
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+.highlight .sx { color: #C65D09 } /* Literal.String.Other */
 .highlight .sr { color: #235388 } /* Literal.String.Regex */
-.highlight .s1 { color: #4070a0 } /* Literal.String.Single */
+.highlight .s1 { color: #4070A0 } /* Literal.String.Single */
 .highlight .ss { color: #517918 } /* Literal.String.Symbol */
 .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
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-.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
-.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
+.highlight .fm { color: #06287E } /* Name.Function.Magic */
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 .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
 @media not print {
 body[data-theme="dark"] .highlight pre { line-height: 125%; }
@@ -80,85 +80,85 @@ body[data-theme="dark"] .highlight span.linenos { color: #aaaaaa; background-col
 body[data-theme="dark"] .highlight td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 body[data-theme="dark"] .highlight span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 body[data-theme="dark"] .highlight .hll { background-color: #404040 }
-body[data-theme="dark"] .highlight { background: #202020; color: #d0d0d0 }
-body[data-theme="dark"] .highlight .c { color: #ababab; font-style: italic } /* Comment */
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-body[data-theme="dark"] .highlight .cpf { color: #ababab; font-style: italic } /* Comment.PreprocFile */
-body[data-theme="dark"] .highlight .c1 { color: #ababab; font-style: italic } /* Comment.Single */
-body[data-theme="dark"] .highlight .cs { color: #e50808; font-weight: bold; background-color: #520000 } /* Comment.Special */
-body[data-theme="dark"] .highlight .gd { color: #ff3a3a } /* Generic.Deleted */
-body[data-theme="dark"] .highlight .ge { color: #d0d0d0; font-style: italic } /* Generic.Emph */
-body[data-theme="dark"] .highlight .ges { color: #d0d0d0; font-weight: bold; font-style: italic } /* Generic.EmphStrong */
-body[data-theme="dark"] .highlight .gr { color: #ff3a3a } /* Generic.Error */
-body[data-theme="dark"] .highlight .gh { color: #ffffff; font-weight: bold } /* Generic.Heading */
+body[data-theme="dark"] .highlight { background: #202020; color: #D0D0D0 }
+body[data-theme="dark"] .highlight .c { color: #ABABAB; font-style: italic } /* Comment */
+body[data-theme="dark"] .highlight .err { color: #A61717; background-color: #E3D2D2 } /* Error */
+body[data-theme="dark"] .highlight .esc { color: #D0D0D0 } /* Escape */
+body[data-theme="dark"] .highlight .g { color: #D0D0D0 } /* Generic */
+body[data-theme="dark"] .highlight .k { color: #6EBF26; font-weight: bold } /* Keyword */
+body[data-theme="dark"] .highlight .l { color: #D0D0D0 } /* Literal */
+body[data-theme="dark"] .highlight .n { color: #D0D0D0 } /* Name */
+body[data-theme="dark"] .highlight .o { color: #D0D0D0 } /* Operator */
+body[data-theme="dark"] .highlight .x { color: #D0D0D0 } /* Other */
+body[data-theme="dark"] .highlight .p { color: #D0D0D0 } /* Punctuation */
+body[data-theme="dark"] .highlight .ch { color: #ABABAB; font-style: italic } /* Comment.Hashbang */
+body[data-theme="dark"] .highlight .cm { color: #ABABAB; font-style: italic } /* Comment.Multiline */
+body[data-theme="dark"] .highlight .cp { color: #FF3A3A; font-weight: bold } /* Comment.Preproc */
+body[data-theme="dark"] .highlight .cpf { color: #ABABAB; font-style: italic } /* Comment.PreprocFile */
+body[data-theme="dark"] .highlight .c1 { color: #ABABAB; font-style: italic } /* Comment.Single */
+body[data-theme="dark"] .highlight .cs { color: #E50808; font-weight: bold; background-color: #520000 } /* Comment.Special */
+body[data-theme="dark"] .highlight .gd { color: #FF3A3A } /* Generic.Deleted */
+body[data-theme="dark"] .highlight .ge { color: #D0D0D0; font-style: italic } /* Generic.Emph */
+body[data-theme="dark"] .highlight .ges { color: #D0D0D0; font-weight: bold; font-style: italic } /* Generic.EmphStrong */
+body[data-theme="dark"] .highlight .gr { color: #FF3A3A } /* Generic.Error */
+body[data-theme="dark"] .highlight .gh { color: #FFF; font-weight: bold } /* Generic.Heading */
 body[data-theme="dark"] .highlight .gi { color: #589819 } /* Generic.Inserted */
-body[data-theme="dark"] .highlight .go { color: #cccccc } /* Generic.Output */
-body[data-theme="dark"] .highlight .gp { color: #aaaaaa } /* Generic.Prompt */
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-body[data-theme="dark"] .highlight .gu { color: #ffffff; text-decoration: underline } /* Generic.Subheading */
-body[data-theme="dark"] .highlight .gt { color: #ff3a3a } /* Generic.Traceback */
-body[data-theme="dark"] .highlight .kc { color: #6ebf26; font-weight: bold } /* Keyword.Constant */
-body[data-theme="dark"] .highlight .kd { color: #6ebf26; font-weight: bold } /* Keyword.Declaration */
-body[data-theme="dark"] .highlight .kn { color: #6ebf26; font-weight: bold } /* Keyword.Namespace */
-body[data-theme="dark"] .highlight .kp { color: #6ebf26 } /* Keyword.Pseudo */
-body[data-theme="dark"] .highlight .kr { color: #6ebf26; font-weight: bold } /* Keyword.Reserved */
-body[data-theme="dark"] .highlight .kt { color: #6ebf26; font-weight: bold } /* Keyword.Type */
-body[data-theme="dark"] .highlight .ld { color: #d0d0d0 } /* Literal.Date */
-body[data-theme="dark"] .highlight .m { color: #51b2fd } /* Literal.Number */
-body[data-theme="dark"] .highlight .s { color: #ed9d13 } /* Literal.String */
-body[data-theme="dark"] .highlight .na { color: #bbbbbb } /* Name.Attribute */
-body[data-theme="dark"] .highlight .nb { color: #2fbccd } /* Name.Builtin */
-body[data-theme="dark"] .highlight .nc { color: #71adff; text-decoration: underline } /* Name.Class */
-body[data-theme="dark"] .highlight .no { color: #40ffff } /* Name.Constant */
-body[data-theme="dark"] .highlight .nd { color: #ffa500 } /* Name.Decorator */
-body[data-theme="dark"] .highlight .ni { color: #d0d0d0 } /* Name.Entity */
-body[data-theme="dark"] .highlight .ne { color: #bbbbbb } /* Name.Exception */
-body[data-theme="dark"] .highlight .nf { color: #71adff } /* Name.Function */
-body[data-theme="dark"] .highlight .nl { color: #d0d0d0 } /* Name.Label */
-body[data-theme="dark"] .highlight .nn { color: #71adff; text-decoration: underline } /* Name.Namespace */
-body[data-theme="dark"] .highlight .nx { color: #d0d0d0 } /* Name.Other */
-body[data-theme="dark"] .highlight .py { color: #d0d0d0 } /* Name.Property */
-body[data-theme="dark"] .highlight .nt { color: #6ebf26; font-weight: bold } /* Name.Tag */
-body[data-theme="dark"] .highlight .nv { color: #40ffff } /* Name.Variable */
-body[data-theme="dark"] .highlight .ow { color: #6ebf26; font-weight: bold } /* Operator.Word */
-body[data-theme="dark"] .highlight .pm { color: #d0d0d0 } /* Punctuation.Marker */
-body[data-theme="dark"] .highlight .w { color: #666666 } /* Text.Whitespace */
-body[data-theme="dark"] .highlight .mb { color: #51b2fd } /* Literal.Number.Bin */
-body[data-theme="dark"] .highlight .mf { color: #51b2fd } /* Literal.Number.Float */
-body[data-theme="dark"] .highlight .mh { color: #51b2fd } /* Literal.Number.Hex */
-body[data-theme="dark"] .highlight .mi { color: #51b2fd } /* Literal.Number.Integer */
-body[data-theme="dark"] .highlight .mo { color: #51b2fd } /* Literal.Number.Oct */
-body[data-theme="dark"] .highlight .sa { color: #ed9d13 } /* Literal.String.Affix */
-body[data-theme="dark"] .highlight .sb { color: #ed9d13 } /* Literal.String.Backtick */
-body[data-theme="dark"] .highlight .sc { color: #ed9d13 } /* Literal.String.Char */
-body[data-theme="dark"] .highlight .dl { color: #ed9d13 } /* Literal.String.Delimiter */
-body[data-theme="dark"] .highlight .sd { color: #ed9d13 } /* Literal.String.Doc */
-body[data-theme="dark"] .highlight .s2 { color: #ed9d13 } /* Literal.String.Double */
-body[data-theme="dark"] .highlight .se { color: #ed9d13 } /* Literal.String.Escape */
-body[data-theme="dark"] .highlight .sh { color: #ed9d13 } /* Literal.String.Heredoc */
-body[data-theme="dark"] .highlight .si { color: #ed9d13 } /* Literal.String.Interpol */
-body[data-theme="dark"] .highlight .sx { color: #ffa500 } /* Literal.String.Other */
-body[data-theme="dark"] .highlight .sr { color: #ed9d13 } /* Literal.String.Regex */
-body[data-theme="dark"] .highlight .s1 { color: #ed9d13 } /* Literal.String.Single */
-body[data-theme="dark"] .highlight .ss { color: #ed9d13 } /* Literal.String.Symbol */
-body[data-theme="dark"] .highlight .bp { color: #2fbccd } /* Name.Builtin.Pseudo */
-body[data-theme="dark"] .highlight .fm { color: #71adff } /* Name.Function.Magic */
-body[data-theme="dark"] .highlight .vc { color: #40ffff } /* Name.Variable.Class */
-body[data-theme="dark"] .highlight .vg { color: #40ffff } /* Name.Variable.Global */
-body[data-theme="dark"] .highlight .vi { color: #40ffff } /* Name.Variable.Instance */
-body[data-theme="dark"] .highlight .vm { color: #40ffff } /* Name.Variable.Magic */
-body[data-theme="dark"] .highlight .il { color: #51b2fd } /* Literal.Number.Integer.Long */
+body[data-theme="dark"] .highlight .go { color: #CCC } /* Generic.Output */
+body[data-theme="dark"] .highlight .gp { color: #AAA } /* Generic.Prompt */
+body[data-theme="dark"] .highlight .gs { color: #D0D0D0; font-weight: bold } /* Generic.Strong */
+body[data-theme="dark"] .highlight .gu { color: #FFF; text-decoration: underline } /* Generic.Subheading */
+body[data-theme="dark"] .highlight .gt { color: #FF3A3A } /* Generic.Traceback */
+body[data-theme="dark"] .highlight .kc { color: #6EBF26; font-weight: bold } /* Keyword.Constant */
+body[data-theme="dark"] .highlight .kd { color: #6EBF26; font-weight: bold } /* Keyword.Declaration */
+body[data-theme="dark"] .highlight .kn { color: #6EBF26; font-weight: bold } /* Keyword.Namespace */
+body[data-theme="dark"] .highlight .kp { color: #6EBF26 } /* Keyword.Pseudo */
+body[data-theme="dark"] .highlight .kr { color: #6EBF26; font-weight: bold } /* Keyword.Reserved */
+body[data-theme="dark"] .highlight .kt { color: #6EBF26; font-weight: bold } /* Keyword.Type */
+body[data-theme="dark"] .highlight .ld { color: #D0D0D0 } /* Literal.Date */
+body[data-theme="dark"] .highlight .m { color: #51B2FD } /* Literal.Number */
+body[data-theme="dark"] .highlight .s { color: #ED9D13 } /* Literal.String */
+body[data-theme="dark"] .highlight .na { color: #BBB } /* Name.Attribute */
+body[data-theme="dark"] .highlight .nb { color: #2FBCCD } /* Name.Builtin */
+body[data-theme="dark"] .highlight .nc { color: #71ADFF; text-decoration: underline } /* Name.Class */
+body[data-theme="dark"] .highlight .no { color: #40FFFF } /* Name.Constant */
+body[data-theme="dark"] .highlight .nd { color: #FFA500 } /* Name.Decorator */
+body[data-theme="dark"] .highlight .ni { color: #D0D0D0 } /* Name.Entity */
+body[data-theme="dark"] .highlight .ne { color: #BBB } /* Name.Exception */
+body[data-theme="dark"] .highlight .nf { color: #71ADFF } /* Name.Function */
+body[data-theme="dark"] .highlight .nl { color: #D0D0D0 } /* Name.Label */
+body[data-theme="dark"] .highlight .nn { color: #71ADFF; text-decoration: underline } /* Name.Namespace */
+body[data-theme="dark"] .highlight .nx { color: #D0D0D0 } /* Name.Other */
+body[data-theme="dark"] .highlight .py { color: #D0D0D0 } /* Name.Property */
+body[data-theme="dark"] .highlight .nt { color: #6EBF26; font-weight: bold } /* Name.Tag */
+body[data-theme="dark"] .highlight .nv { color: #40FFFF } /* Name.Variable */
+body[data-theme="dark"] .highlight .ow { color: #6EBF26; font-weight: bold } /* Operator.Word */
+body[data-theme="dark"] .highlight .pm { color: #D0D0D0 } /* Punctuation.Marker */
+body[data-theme="dark"] .highlight .w { color: #666 } /* Text.Whitespace */
+body[data-theme="dark"] .highlight .mb { color: #51B2FD } /* Literal.Number.Bin */
+body[data-theme="dark"] .highlight .mf { color: #51B2FD } /* Literal.Number.Float */
+body[data-theme="dark"] .highlight .mh { color: #51B2FD } /* Literal.Number.Hex */
+body[data-theme="dark"] .highlight .mi { color: #51B2FD } /* Literal.Number.Integer */
+body[data-theme="dark"] .highlight .mo { color: #51B2FD } /* Literal.Number.Oct */
+body[data-theme="dark"] .highlight .sa { color: #ED9D13 } /* Literal.String.Affix */
+body[data-theme="dark"] .highlight .sb { color: #ED9D13 } /* Literal.String.Backtick */
+body[data-theme="dark"] .highlight .sc { color: #ED9D13 } /* Literal.String.Char */
+body[data-theme="dark"] .highlight .dl { color: #ED9D13 } /* Literal.String.Delimiter */
+body[data-theme="dark"] .highlight .sd { color: #ED9D13 } /* Literal.String.Doc */
+body[data-theme="dark"] .highlight .s2 { color: #ED9D13 } /* Literal.String.Double */
+body[data-theme="dark"] .highlight .se { color: #ED9D13 } /* Literal.String.Escape */
+body[data-theme="dark"] .highlight .sh { color: #ED9D13 } /* Literal.String.Heredoc */
+body[data-theme="dark"] .highlight .si { color: #ED9D13 } /* Literal.String.Interpol */
+body[data-theme="dark"] .highlight .sx { color: #FFA500 } /* Literal.String.Other */
+body[data-theme="dark"] .highlight .sr { color: #ED9D13 } /* Literal.String.Regex */
+body[data-theme="dark"] .highlight .s1 { color: #ED9D13 } /* Literal.String.Single */
+body[data-theme="dark"] .highlight .ss { color: #ED9D13 } /* Literal.String.Symbol */
+body[data-theme="dark"] .highlight .bp { color: #2FBCCD } /* Name.Builtin.Pseudo */
+body[data-theme="dark"] .highlight .fm { color: #71ADFF } /* Name.Function.Magic */
+body[data-theme="dark"] .highlight .vc { color: #40FFFF } /* Name.Variable.Class */
+body[data-theme="dark"] .highlight .vg { color: #40FFFF } /* Name.Variable.Global */
+body[data-theme="dark"] .highlight .vi { color: #40FFFF } /* Name.Variable.Instance */
+body[data-theme="dark"] .highlight .vm { color: #40FFFF } /* Name.Variable.Magic */
+body[data-theme="dark"] .highlight .il { color: #51B2FD } /* Literal.Number.Integer.Long */
 @media (prefers-color-scheme: dark) {
 body:not([data-theme="light"]) .highlight pre { line-height: 125%; }
 body:not([data-theme="light"]) .highlight td.linenos .normal { color: #aaaaaa; background-color: transparent; padding-left: 5px; padding-right: 5px; }
@@ -166,84 +166,84 @@ body:not([data-theme="light"]) .highlight span.linenos { color: #aaaaaa; backgro
 body:not([data-theme="light"]) .highlight td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 body:not([data-theme="light"]) .highlight span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 body:not([data-theme="light"]) .highlight .hll { background-color: #404040 }
-body:not([data-theme="light"]) .highlight { background: #202020; color: #d0d0d0 }
-body:not([data-theme="light"]) .highlight .c { color: #ababab; font-style: italic } /* Comment */
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-body:not([data-theme="light"]) .highlight .esc { color: #d0d0d0 } /* Escape */
-body:not([data-theme="light"]) .highlight .g { color: #d0d0d0 } /* Generic */
-body:not([data-theme="light"]) .highlight .k { color: #6ebf26; font-weight: bold } /* Keyword */
-body:not([data-theme="light"]) .highlight .l { color: #d0d0d0 } /* Literal */
-body:not([data-theme="light"]) .highlight .n { color: #d0d0d0 } /* Name */
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diff --git a/api/modules.html b/api/modules.html
index 2995928..1d0b03a 100644
--- a/api/modules.html
+++ b/api/modules.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -254,6 +254,10 @@ <h1>singler<a class="headerlink" href="#singler" title="Link to this heading">¶
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="singler.html">singler package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="singler.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="singler.html#module-singler.aggregate_reference">singler.aggregate_reference module</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="singler.html#singler.aggregate_reference.aggregate_reference"><code class="docutils literal notranslate"><span class="pre">aggregate_reference()</span></code></a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="singler.html#module-singler.annotate_integrated">singler.annotate_integrated module</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="singler.html#singler.annotate_integrated.annotate_integrated"><code class="docutils literal notranslate"><span class="pre">annotate_integrated()</span></code></a></li>
 </ul>
diff --git a/api/singler.html b/api/singler.html
index 5ac2caa..031a746 100644
--- a/api/singler.html
+++ b/api/singler.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler package - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -252,6 +252,50 @@
 <span id="singler-package"></span><h1>singler package<a class="headerlink" href="#module-singler" title="Link to this heading">¶</a></h1>
 <section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading">¶</a></h2>
+</section>
+<section id="module-singler.aggregate_reference">
+<span id="singler-aggregate-reference-module"></span><h2>singler.aggregate_reference module<a class="headerlink" href="#module-singler.aggregate_reference" title="Link to this heading">¶</a></h2>
+<dl class="py function">
+<dt class="sig sig-object py" id="singler.aggregate_reference.aggregate_reference">
+<span class="sig-prename descclassname"><span class="pre">singler.aggregate_reference.</span></span><span class="sig-name descname"><span class="pre">aggregate_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_labels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_features</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_centers</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">power</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_top</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rank</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assay_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'logcounts'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subset_row</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_missing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_threads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/singler/aggregate_reference.html#aggregate_reference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#singler.aggregate_reference.aggregate_reference" title="Link to this definition">¶</a></dt>
+<dd><p>Aggregate reference samples for a given label by using vector quantization to average their count profiles.
+The idea is to reduce the size of single-cell reference datasets so as to reduce the computation time of <a class="reference internal" href="#singler.train_single.train_single" title="singler.train_single.train_single"><code class="xref py py-func docutils literal notranslate"><span class="pre">train_single()</span></code></a>.
+We perform k-means clustering for all cells in each label and aggregate all cells within each k-means cluster.
+(More specifically, the clustering is done on the principal components generated from the highly variable genes to better capture the structure within each label.)
+This yields one or more profiles per label, reducing the number of separate observations while preserving some level of intra-label heterogeneity.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ref_data</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Any" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Any</span></code></a></span>) – Floating-point matrix of reference expression values, usually containing log-expression values.
+Alternatively, a <a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a> object containing such a matrix.</p></li>
+<li><p><strong>ref_labels</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Sequence" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Sequence</span></code></a></span>) – Array of length equal to the number of columns in <code class="docutils literal notranslate"><span class="pre">ref_data</span></code>, containing the labels for each cell.</p></li>
+<li><p><strong>ref_features</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Sequence" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Sequence</span></code></a></span>) – Sequence of identifiers for each feature, i.e., row in <code class="docutils literal notranslate"><span class="pre">ref_data</span></code>.</p></li>
+<li><p><strong>num_centers</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Optional" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Maximum number of aggregated profiles to produce for each label with <code class="xref py py-func docutils literal notranslate"><span class="pre">cluster_kmeans()</span></code>.
+If <code class="docutils literal notranslate"><span class="pre">None</span></code>, a suitable number of profiles is automatically chosen.</p></li>
+<li><p><strong>power</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#float" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></span>) – Number between 0 and 1 indicating how much aggregation should be performed.
+Specifically, we set the number of clusters to <code class="docutils literal notranslate"><span class="pre">X**power</span></code> where <code class="docutils literal notranslate"><span class="pre">X</span></code> is the number of cells assigned to that label.
+Ignored if <code class="docutils literal notranslate"><span class="pre">num_centers</span></code> is not <code class="docutils literal notranslate"><span class="pre">None</span></code>.</p></li>
+<li><p><strong>num_top</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></span>) – Number of highly variable genes to use for PCA prior to clustering, see <code class="xref py py-func docutils literal notranslate"><span class="pre">choose_highly_variable_genes()</span></code>.</p></li>
+<li><p><strong>rank</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></span>) – Number of principal components to use during clustering, see <code class="xref py py-func docutils literal notranslate"><span class="pre">run_pca()</span></code>.</p></li>
+<li><p><strong>assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>]</span>) – Integer or string specifying the assay of <code class="docutils literal notranslate"><span class="pre">ref_data</span></code> containing the relevant expression matrix,
+if <code class="docutils literal notranslate"><span class="pre">ref</span></code> is a <a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a> object.</p></li>
+<li><p><strong>subset_row</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Optional" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Sequence" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Sequence</span></code></a>]</span>) – Array of row indices specifying the rows of <code class="docutils literal notranslate"><span class="pre">ref_data</span></code> to use for clustering.
+If <code class="docutils literal notranslate"><span class="pre">None</span></code>, no additional filtering is performed.
+Note that even if <code class="docutils literal notranslate"><span class="pre">subset_row</span></code> is provided, aggregation is still performed on all genes.</p></li>
+<li><p><strong>check_missing</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#bool" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></span>) – Whether to check for and remove rows with missing (NaN) values from <code class="docutils literal notranslate"><span class="pre">ref_data</span></code>.</p></li>
+<li><p><strong>num_threads</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></span>) – Number of threads to use.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Return type<span class="colon">:</span></dt>
+<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a></span></p>
+</dd>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>A <a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a> containing the aggregated values in its first assay.
+The label for each aggregated profile is stored in the column data.</p>
+</dd>
+</dl>
+</dd></dl>
+
 </section>
 <section id="module-singler.annotate_integrated">
 <span id="singler-annotate-integrated-module"></span><h2>singler.annotate_integrated module<a class="headerlink" href="#module-singler.annotate_integrated" title="Link to this heading">¶</a></h2>
@@ -268,7 +312,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 features and columns are samples (usually cells). Entries should be
 expression values; only the ranking within each column is used.</p>
 <p>Alternatively, a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 containing such a matrix in one of its assays.</p>
 </p></li>
 <li><p><strong>ref_data</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Sequence" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Sequence</span></code></a></span>) – <p>Sequence consisting of one or more of the following:</p>
@@ -296,10 +340,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <code class="docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code> objects.</p>
 </p></li>
 <li><p><strong>test_assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Assay of <code class="docutils literal notranslate"><span class="pre">test_data</span></code> containing the expression matrix, if <code class="docutils literal notranslate"><span class="pre">test_data</span></code> is a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
 <li><p><strong>test_check_missing</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#bool" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></span>) – Whether to check for and remove missing (i.e., NaN) values from the test dataset.</p></li>
 <li><p><strong>ref_assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Assay containing the expression matrix for any entry of <code class="docutils literal notranslate"><span class="pre">ref_data</span></code> that is a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
 <li><p><strong>ref_check_missing</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#bool" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></span>) – Whether to check for and remove missing (i.e., NaN) values from the reference datasets.</p></li>
 <li><p><strong>train_single_args</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#dict" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></span>) – Further arguments to pass to
 <a class="reference internal" href="#singler.train_single.train_single" title="singler.train_single.train_single"><code class="xref py py-func docutils literal notranslate"><span class="pre">train_single()</span></code></a>.</p></li>
@@ -313,7 +357,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Tuple" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Tuple</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#list" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>[<a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a>], <a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a>]</span></p>
+<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Tuple" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Tuple</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#list" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>[<a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a>], <a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a>]</span></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p>Tuple where the first element contains per-reference results (i.e. a
@@ -341,7 +385,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 features and columns are samples (usually cells). Entries should be expression
 values; only the ranking within each column will be used.</p>
 <p>Alternatively, a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 containing such a matrix in one of its assays. Non-default assay
 types can be specified in <code class="docutils literal notranslate"><span class="pre">classify_args</span></code>.</p>
 </p></li>
@@ -350,7 +394,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 usually log-transformed (see comments for the <code class="docutils literal notranslate"><span class="pre">ref</span></code> argument in
 <a class="reference internal" href="#singler.train_single.train_single" title="singler.train_single.train_single"><code class="xref py py-func docutils literal notranslate"><span class="pre">train_single()</span></code></a>).</p>
 <p>Alternatively, a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 containing such a matrix in one of its assays. Non-default assay
 types can be specified in <code class="docutils literal notranslate"><span class="pre">classify_args</span></code>.</p>
 </p></li>
@@ -363,9 +407,9 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 containing the feature identifier for each row. Alternatively
 <code class="docutils literal notranslate"><span class="pre">None</span></code>, to use the row names of the experiment as features.</p></li>
 <li><p><strong>test_assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Assay containing the expression matrix, if <code class="docutils literal notranslate"><span class="pre">test_data</span></code> is a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
 <li><p><strong>ref_assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Assay containing the expression matrix, if <code class="docutils literal notranslate"><span class="pre">ref_data</span></code> is a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
 <li><p><strong>test_assay_type</strong> – Whether to remove rows with missing values from the test dataset.</p></li>
 <li><p><strong>ref_assay_type</strong> – Whether to remove rows with missing values from the reference dataset.</p></li>
 <li><p><strong>train_args</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#dict" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></span>) – Further arguments to pass to
@@ -376,10 +420,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a></span></p>
+<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a></span></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
-<dd class="field-odd"><p>A <a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a> of labelling results, see
+<dd class="field-odd"><p>A <a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a> of labelling results, see
 <a class="reference internal" href="#singler.classify_single.classify_single" title="singler.classify_single.classify_single"><code class="xref py py-func docutils literal notranslate"><span class="pre">classify_single()</span></code></a> for details.</p>
 </dd>
 </dl>
@@ -400,17 +444,17 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 Normalized and/or transformed expression values are also acceptable as only
 the ranking is used within this function.</p>
 <p>Alternatively, a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 containing such a matrix in one of its assays.</p>
 </p></li>
-<li><p><strong>results</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#list" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>[<a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a>]</span>) – List of classification results generated by running
+<li><p><strong>results</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#list" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>[<a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a>]</span>) – List of classification results generated by running
 <a class="reference internal" href="#singler.classify_single.classify_single" title="singler.classify_single.classify_single"><code class="xref py py-func docutils literal notranslate"><span class="pre">classify_single()</span></code></a> on
 <code class="docutils literal notranslate"><span class="pre">test_data</span></code> with each reference. References should be in the
 same order as that used to construct <code class="docutils literal notranslate"><span class="pre">integrated_prebuilt</span></code>.</p></li>
 <li><p><strong>integrated_prebuilt</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference internal" href="#singler.train_integrated.TrainedIntegratedReferences" title="singler.train_integrated.TrainedIntegratedReferences"><code class="xref py py-class docutils literal notranslate"><span class="pre">TrainedIntegratedReferences</span></code></a></span>) – Integrated reference object, constructed with
 <a class="reference internal" href="#singler.train_integrated.train_integrated" title="singler.train_integrated.train_integrated"><code class="xref py py-func docutils literal notranslate"><span class="pre">train_integrated()</span></code></a>.</p></li>
 <li><p><strong>assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Assay containing the expression matrix, if <code class="docutils literal notranslate"><span class="pre">test_data</span></code> is a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
 <li><p><strong>quantile</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#float" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></span>) – Quantile of the correlation distribution for computing the score for each label.
 Larger values increase sensitivity of matches at the expense of
 similarity to the average behavior of each label.</p></li>
@@ -424,10 +468,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a></span></p>
+<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a></span></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
-<dd class="field-odd"><p>A <a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a> containing the
+<dd class="field-odd"><p>A <a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a> containing the
 <code class="docutils literal notranslate"><span class="pre">best_label</span></code> across all references, defined as the assigned label in
 the best reference; the identity of the <code class="docutils literal notranslate"><span class="pre">best_reference</span></code>, either as a
 name string or an integer index; the <code class="docutils literal notranslate"><span class="pre">scores</span></code> for the best label in
@@ -454,13 +498,13 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 Normalized and transformed expression values are also acceptable as only
 the ranking is used within this function.</p>
 <p>Alternatively, a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 containing such a matrix in one of its assays.</p>
 </p></li>
 <li><p><strong>ref_prebuilt</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference internal" href="#singler.train_single.TrainedSingleReference" title="singler.train_single.TrainedSingleReference"><code class="xref py py-class docutils literal notranslate"><span class="pre">TrainedSingleReference</span></code></a></span>) – A pre-built reference created with
 <a class="reference internal" href="#singler.train_single.train_single" title="singler.train_single.train_single"><code class="xref py py-func docutils literal notranslate"><span class="pre">train_single()</span></code></a>.</p></li>
 <li><p><strong>assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Assay containing the expression matrix, if <code class="docutils literal notranslate"><span class="pre">test_data</span></code> is a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
 <li><p><strong>quantile</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#float" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></span>) – Quantile of the correlation distribution for computing the score for each label.
 Larger values increase sensitivity of matches at the expense of
 similarity to the average behavior of each label.</p></li>
@@ -472,7 +516,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.5.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a></span></p>
+<dd class="field-even"><p><span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://biocpy.github.io/BiocFrame/api/biocframe.html#biocframe.BiocFrame.BiocFrame" title="(in BiocFrame v0.6.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code></a></span></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p>A <code class="xref py py-class docutils literal notranslate"><span class="pre">BiocFrame</span></code> containing the <code class="docutils literal notranslate"><span class="pre">best</span></code>
@@ -500,7 +544,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 values of a reference dataset.  Each column is a sample and each
 row is a feature.</p>
 <p>Alternatively, this can be a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 containing a matrix-like object in one of its assays.</p>
 <p>Alternatively, a list of such matrices or <code class="docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code>
 objects, typically for multiple batches of the same reference; it
@@ -522,7 +566,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 equal to the number of rows of the corresponding entry of <code class="docutils literal notranslate"><span class="pre">ref</span></code>.</p>
 </p></li>
 <li><p><strong>assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Name or index of the assay of interest, if <code class="docutils literal notranslate"><span class="pre">ref</span></code> is or contains
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 objects.</p></li>
 <li><p><strong>check_missing</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#bool" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></span>) – Whether to check for and remove rows with missing (NaN) values in
 the reference matrices. This can be set to False if it is known
@@ -567,7 +611,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <span id="singler-train-integrated-module"></span><h2>singler.train_integrated module<a class="headerlink" href="#module-singler.train_integrated" title="Link to this heading">¶</a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="singler.train_integrated.TrainedIntegratedReferences">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">singler.train_integrated.</span></span><span class="sig-name descname"><span class="pre">TrainedIntegratedReferences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ptr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_labels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_num_features</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/singler/train_integrated.html#TrainedIntegratedReferences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#singler.train_integrated.TrainedIntegratedReferences" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">singler.train_integrated.</span></span><span class="sig-name descname"><span class="pre">TrainedIntegratedReferences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ptr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_labels</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/singler/train_integrated.html#TrainedIntegratedReferences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#singler.train_integrated.TrainedIntegratedReferences" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p>Object containing integrated references, typically constructed by
 <a class="reference internal" href="#singler.train_integrated.train_integrated" title="singler.train_integrated.train_integrated"><code class="xref py py-meth docutils literal notranslate"><span class="pre">train_integrated()</span></code></a>.</p>
@@ -611,7 +655,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <span id="singler-train-single-module"></span><h2>singler.train_single module<a class="headerlink" href="#module-singler.train_single" title="Link to this heading">¶</a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="singler.train_single.TrainedSingleReference">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">singler.train_single.</span></span><span class="sig-name descname"><span class="pre">TrainedSingleReference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ptr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_label_codes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">features</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">markers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_num_features</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/singler/train_single.html#TrainedSingleReference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#singler.train_single.TrainedSingleReference" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">singler.train_single.</span></span><span class="sig-name descname"><span class="pre">TrainedSingleReference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ptr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_label_codes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">features</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">markers</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/singler/train_single.html#TrainedSingleReference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#singler.train_single.TrainedSingleReference" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p>A prebuilt reference object, typically created by
 <a class="reference internal" href="#singler.train_single.train_single" title="singler.train_single.train_single"><code class="xref py py-meth docutils literal notranslate"><span class="pre">train_single()</span></code></a>. This is intended for
@@ -685,7 +729,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py function">
 <dt class="sig sig-object py" id="singler.train_single.train_single">
-<span class="sig-prename descclassname"><span class="pre">singler.train_single.</span></span><span class="sig-name descname"><span class="pre">train_single</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_labels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_features</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_features=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assay_type='logcounts'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restrict_to=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_missing=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">markers=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">marker_method='classic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">marker_args={}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nn_parameters=&lt;knncolle.vptree.VptreeParameters</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_threads=1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/singler/train_single.html#train_single"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#singler.train_single.train_single" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">singler.train_single.</span></span><span class="sig-name descname"><span class="pre">train_single</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_labels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_features</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_features=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assay_type='logcounts'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restrict_to=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_missing=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">markers=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">marker_method='classic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_de=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">marker_args={}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregate=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregate_args={}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nn_parameters=&lt;knncolle.vptree.VptreeParameters</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_threads=1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/singler/train_single.html#train_single"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#singler.train_single.train_single" title="Link to this definition">¶</a></dt>
 <dd><p>Build a single reference dataset in preparation for classification.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -697,7 +741,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 differential expression analyses. Otherwise, any expression values
 are acceptable as only the ranking within each column is used.</p>
 <p>Alternatively, a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>
 containing such a matrix in one of its assays.</p>
 </p></li>
 <li><p><strong>ref_labels</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Sequence" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Sequence</span></code></a></span>) – Sequence of labels for each reference profile, i.e., column in <code class="docutils literal notranslate"><span class="pre">ref_data</span></code>.</p></li>
@@ -705,7 +749,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li><p><strong>test_features</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Optional" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Sequence" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Sequence</span></code></a>]</span>) – Sequence of identifiers for each feature in the test dataset.</p></li>
 <li><p><strong>assay_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#str" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Assay containing the expression matrix,
 if <code class="docutils literal notranslate"><span class="pre">ref_data</span></code> is a
-<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.4.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
+<a class="reference external" href="https://biocpy.github.io/SummarizedExperiment/api/summarizedexperiment.html#summarizedexperiment.SummarizedExperiment.SummarizedExperiment" title="(in SummarizedExperiment v0.5.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SummarizedExperiment</span></code></a>.</p></li>
 <li><p><strong>check_missing</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#bool" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></span>) – Whether to check for and remove rows with missing (NaN) values
 from <code class="docutils literal notranslate"><span class="pre">ref_data</span></code>.</p></li>
 <li><p><strong>restrict_to</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Union" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#set" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">set</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#dict" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a>, <a class="reference external" href="https://docs.python.org/3.12/library/constants.html#None" title="(in Python v3.12)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code></a>]</span>) – Subset of available features to restrict to. Only features in
@@ -716,12 +760,19 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 that are upregulated in <code class="docutils literal notranslate"><span class="pre">a</span></code> compared to <code class="docutils literal notranslate"><span class="pre">b</span></code>. All such features
 should be present in <code class="docutils literal notranslate"><span class="pre">features</span></code>, and all labels in <code class="docutils literal notranslate"><span class="pre">labels</span></code>
 should have keys in the inner and outer dictionaries.</p></li>
-<li><p><strong>marker_method</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Literal" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Literal</span></code></a>[<code class="docutils literal notranslate"><span class="pre">'classic'</span></code>]</span>) – Method to identify markers from each pairwise comparisons between
-labels in <code class="docutils literal notranslate"><span class="pre">ref_data</span></code>.  If “classic”, we call
-<a class="reference internal" href="#singler.get_classic_markers.get_classic_markers" title="singler.get_classic_markers.get_classic_markers"><code class="xref py py-meth docutils literal notranslate"><span class="pre">get_classic_markers()</span></code></a>.
+<li><p><strong>marker_method</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Literal" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Literal</span></code></a>[<code class="docutils literal notranslate"><span class="pre">'classic'</span></code>, <code class="docutils literal notranslate"><span class="pre">'auc'</span></code>, <code class="docutils literal notranslate"><span class="pre">'cohens_d'</span></code>]</span>) – Method to identify markers from each pairwise comparisons between labels in <code class="docutils literal notranslate"><span class="pre">ref_data</span></code>.
+If <code class="docutils literal notranslate"><span class="pre">classic</span></code>, we call <a class="reference internal" href="#singler.get_classic_markers.get_classic_markers" title="singler.get_classic_markers.get_classic_markers"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_classic_markers()</span></code></a>.
+If <code class="docutils literal notranslate"><span class="pre">auc</span></code> or <code class="docutils literal notranslate"><span class="pre">cohens_d</span></code>, we call <code class="xref py py-func docutils literal notranslate"><span class="pre">score_markers()</span></code>.
+Only used if <code class="docutils literal notranslate"><span class="pre">markers</span></code> is not supplied.</p></li>
+<li><p><strong>num_de</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Optional" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code></a>[<a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>]</span>) – Number of differentially expressed genes to use as markers for each pairwise comparison between labels.
+If <code class="docutils literal notranslate"><span class="pre">None</span></code> and <code class="docutils literal notranslate"><span class="pre">marker_method</span> <span class="pre">=</span> <span class="pre">&quot;classic&quot;</span></code>, an appropriate number of genes is determined by <a class="reference internal" href="#singler.get_classic_markers.get_classic_markers" title="singler.get_classic_markers.get_classic_markers"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_classic_markers()</span></code></a>.
+Otherwise, it is set to 10.
 Only used if <code class="docutils literal notranslate"><span class="pre">markers</span></code> is not supplied.</p></li>
 <li><p><strong>marker_args</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#dict" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></span>) – Further arguments to pass to the chosen marker detection method.
+If <code class="docutils literal notranslate"><span class="pre">marker_method</span> <span class="pre">=</span> <span class="pre">&quot;classic&quot;</span></code>, this is <a class="reference internal" href="#singler.get_classic_markers.get_classic_markers" title="singler.get_classic_markers.get_classic_markers"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_classic_markers()</span></code></a>, otherwise it is <code class="xref py py-func docutils literal notranslate"><span class="pre">score_markers()</span></code>.
 Only used if <code class="docutils literal notranslate"><span class="pre">markers</span></code> is not supplied.</p></li>
+<li><p><strong>aggregate</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#bool" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></span>) – Whether the reference dataset should be aggregated to pseudo-bulk samples for speed, see <a class="reference internal" href="#singler.aggregate_reference.aggregate_reference" title="singler.aggregate_reference.aggregate_reference"><code class="xref py py-func docutils literal notranslate"><span class="pre">aggregate_reference()</span></code></a> for details.</p></li>
+<li><p><strong>aggregate_args</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/stdtypes.html#dict" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></span>) – Further arguments to pass to <a class="reference internal" href="#singler.aggregate_reference.aggregate_reference" title="singler.aggregate_reference.aggregate_reference"><code class="xref py py-func docutils literal notranslate"><span class="pre">aggregate_reference()</span></code></a> when <code class="docutils literal notranslate"><span class="pre">aggregate</span> <span class="pre">=</span> <span class="pre">True</span></code>.</p></li>
 <li><p><strong>nn_parameters</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/typing.html#typing.Optional" title="(in Python v3.12)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code></a>[<code class="xref py py-class docutils literal notranslate"><span class="pre">Parameters</span></code>]</span>) – Algorithm for constructing the neighbor search index, used to
 compute scores during classification.</p></li>
 <li><p><strong>num_threads</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.12/library/functions.html#int" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></span>) – Number of threads to use for reference building.</p></li>
@@ -789,6 +840,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
             <ul>
 <li><a class="reference internal" href="#">singler package</a><ul>
 <li><a class="reference internal" href="#submodules">Submodules</a></li>
+<li><a class="reference internal" href="#module-singler.aggregate_reference">singler.aggregate_reference module</a><ul>
+<li><a class="reference internal" href="#singler.aggregate_reference.aggregate_reference"><code class="docutils literal notranslate"><span class="pre">aggregate_reference()</span></code></a></li>
+</ul>
+</li>
 <li><a class="reference internal" href="#module-singler.annotate_integrated">singler.annotate_integrated module</a><ul>
 <li><a class="reference internal" href="#singler.annotate_integrated.annotate_integrated"><code class="docutils literal notranslate"><span class="pre">annotate_integrated()</span></code></a></li>
 </ul>
diff --git a/authors.html b/authors.html
index 4be8902..2df0591 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Contributors - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
diff --git a/changelog.html b/changelog.html
index 076fc27..2bbee2b 100644
--- a/changelog.html
+++ b/changelog.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Changelog - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -250,6 +250,14 @@
         <article role="main" id="furo-main-content">
           <section class="tex2jax_ignore mathjax_ignore" id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Link to this heading">¶</a></h1>
+<section id="version-0-4-1">
+<h2>Version 0.4.1<a class="headerlink" href="#version-0-4-1" title="Link to this heading">¶</a></h2>
+<ul class="simple">
+<li><p>Added the <code class="docutils literal notranslate"><span class="pre">aggregate_reference()</span></code> function to aggregate references for speed.
+This is conveniently used via the <code class="docutils literal notranslate"><span class="pre">aggregate=</span></code> option in <code class="docutils literal notranslate"><span class="pre">train_single()</span></code>.</p></li>
+<li><p>Extend <code class="docutils literal notranslate"><span class="pre">train_single()</span></code> to support marker detection using <strong>scrapper</strong> to compute Cohen’s d or the AUC of each pairwise comparison.</p></li>
+</ul>
+</section>
 <section id="version-0-4-0">
 <h2>Version 0.4.0<a class="headerlink" href="#version-0-4-0" title="Link to this heading">¶</a></h2>
 <ul class="simple">
@@ -341,6 +349,7 @@ <h2>Version 0.1.0<a class="headerlink" href="#version-0-1-0" title="Link to this
           <div class="toc-tree">
             <ul>
 <li><a class="reference internal" href="#">Changelog</a><ul>
+<li><a class="reference internal" href="#version-0-4-1">Version 0.4.1</a></li>
 <li><a class="reference internal" href="#version-0-4-0">Version 0.4.0</a></li>
 <li><a class="reference internal" href="#version-0-3-0">Version 0.3.0</a></li>
 <li><a class="reference internal" href="#version-0-2-0">Version 0.2.0</a></li>
diff --git a/contributing.html b/contributing.html
index f167f13..c19fbc4 100644
--- a/contributing.html
+++ b/contributing.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Contributing - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
diff --git a/genindex.html b/genindex.html
index 92772f5..d2e543a 100644
--- a/genindex.html
+++ b/genindex.html
@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="#" /><link rel="search" title="Search" href="search.html" />
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 --><title>Index - singler unknown documentation</title>
-<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -249,10 +249,12 @@ <h1 id="index">Index</h1>
   <h2>A</h2>
   <table style="width: 100%" class="indextable genindextable"><tr>
     <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="api/singler.html#singler.annotate_integrated.annotate_integrated">annotate_integrated() (in module singler.annotate_integrated)</a>
+        <li><a href="api/singler.html#singler.aggregate_reference.aggregate_reference">aggregate_reference() (in module singler.aggregate_reference)</a>
 </li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="api/singler.html#singler.annotate_integrated.annotate_integrated">annotate_integrated() (in module singler.annotate_integrated)</a>
+</li>
         <li><a href="api/singler.html#singler.annotate_single.annotate_single">annotate_single() (in module singler.annotate_single)</a>
 </li>
     </ul></td>
@@ -316,6 +318,8 @@ <h2>M</h2>
 
         <ul>
           <li><a href="api/singler.html#module-singler">singler</a>
+</li>
+          <li><a href="api/singler.html#module-singler.aggregate_reference">singler.aggregate_reference</a>
 </li>
           <li><a href="api/singler.html#module-singler.annotate_integrated">singler.annotate_integrated</a>
 </li>
@@ -371,6 +375,13 @@ <h2>S</h2>
 
         <ul>
           <li><a href="api/singler.html#module-singler">module</a>
+</li>
+        </ul></li>
+        <li>
+    singler.aggregate_reference
+
+        <ul>
+          <li><a href="api/singler.html#module-singler.aggregate_reference">module</a>
 </li>
         </ul></li>
         <li>
diff --git a/index.html b/index.html
index 0d7df8d..86ca1d6 100644
--- a/index.html
+++ b/index.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -269,6 +269,7 @@ <h1>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 <li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="authors.html">Authors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-4-1">Version 0.4.1</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-4-0">Version 0.4.0</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-3-0">Version 0.3.0</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-2-0">Version 0.2.0</a></li>
diff --git a/license.html b/license.html
index 44b35a4..2ccf5b9 100644
--- a/license.html
+++ b/license.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>License - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
diff --git a/objects.inv b/objects.inv
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diff --git a/py-modindex.html b/py-modindex.html
index 0a59a3a..a11f713 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" />
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 --><title>Python Module Index - singler unknown documentation</title>
-<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -259,6 +259,12 @@ <h1>Python Module Index</h1>
         <a href="api/singler.html#module-singler"><code class="xref">singler</code></a></td><td>
     <em></em></td>
   </tr>
+  <tr class="cg-1">
+    <td></td>
+    <td>&#160;&#160;&#160;
+        <a href="api/singler.html#module-singler.aggregate_reference"><code class="xref">singler.aggregate_reference</code></a></td><td>
+    <em></em></td>
+  </tr>
   <tr class="cg-1">
     <td></td>
     <td>&#160;&#160;&#160;
diff --git a/readme.html b/readme.html
index 8b58869..53b5614 100644
--- a/readme.html
+++ b/readme.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Tinder for single-cell data - singler unknown documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />
     
@@ -273,7 +273,7 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
 <section id="quick-start">
 <h2>Quick start<a class="headerlink" href="#quick-start" title="Link to this heading">¶</a></h2>
 <p>Firstly, let’s load in the famous PBMC 4k dataset from 10X Genomics:</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">singlecellexperiment</span> <span class="k">as</span> <span class="nn">sce</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">singlecellexperiment</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">sce</span>
 <span class="n">data</span> <span class="o">=</span> <span class="n">sce</span><span class="o">.</span><span class="n">read_tenx_h5</span><span class="p">(</span><span class="s2">&quot;pbmc4k-tenx.h5&quot;</span><span class="p">,</span> <span class="n">realize_assays</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 <span class="n">mat</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">assay</span><span class="p">(</span><span class="s2">&quot;counts&quot;</span><span class="p">)</span>
 <span class="n">features</span> <span class="o">=</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">row_data</span><span class="p">[</span><span class="s2">&quot;name&quot;</span><span class="p">]]</span>
@@ -281,7 +281,7 @@ <h2>Quick start<a class="headerlink" href="#quick-start" title="Link to this hea
 </div>
 <p>or if you are coming from scverse ecosystem, i.e. <code class="docutils literal notranslate"><span class="pre">AnnData</span></code>, simply read the object as <code class="docutils literal notranslate"><span class="pre">SingleCellExperiment</span></code> and extract the matrix and the features.
 Read more on <a class="reference external" href="https://biocpy.github.io/tutorial/chapters/experiments/single_cell_experiment.html">SingleCellExperiment here</a>.</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">singlecellexperiment</span> <span class="k">as</span> <span class="nn">sce</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">singlecellexperiment</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">sce</span>
 
 <span class="n">sce_adata</span> <span class="o">=</span> <span class="n">sce</span><span class="o">.</span><span class="n">SingleCellExperiment</span><span class="o">.</span><span class="n">from_anndata</span><span class="p">(</span><span class="n">adata</span><span class="p">)</span> 
 
@@ -290,13 +290,13 @@ <h2>Quick start<a class="headerlink" href="#quick-start" title="Link to this hea
 </pre></div>
 </div>
 <p>Now, we fetch the Blueprint/ENCODE reference:</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">celldex</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">celldex</span>
 
 <span class="n">ref_data</span> <span class="o">=</span> <span class="n">celldex</span><span class="o">.</span><span class="n">fetch_reference</span><span class="p">(</span><span class="s2">&quot;blueprint_encode&quot;</span><span class="p">,</span> <span class="s2">&quot;2024-02-26&quot;</span><span class="p">,</span> <span class="n">realize_assays</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 </div>
 <p>We can annotate each cell in <code class="docutils literal notranslate"><span class="pre">mat</span></code> with the reference:</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">singler</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">singler</span>
 <span class="n">results</span> <span class="o">=</span> <span class="n">singler</span><span class="o">.</span><span class="n">annotate_single</span><span class="p">(</span>
     <span class="n">test_data</span> <span class="o">=</span> <span class="n">mat</span><span class="p">,</span>
     <span class="n">test_features</span> <span class="o">=</span> <span class="n">features</span><span class="p">,</span>
@@ -360,8 +360,8 @@ <h2>Calling low-level functions<a class="headerlink" href="#calling-low-level-fu
 <section id="integrating-labels-across-references">
 <h2>Integrating labels across references<a class="headerlink" href="#integrating-labels-across-references" title="Link to this heading">¶</a></h2>
 <p>We can use annotations from multiple references through the <code class="docutils literal notranslate"><span class="pre">annotate_integrated()</span></code> function:</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">singler</span>
-<span class="kn">import</span> <span class="nn">celldex</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">singler</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">celldex</span>
 
 <span class="n">blueprint_ref</span> <span class="o">=</span> <span class="n">celldex</span><span class="o">.</span><span class="n">fetch_reference</span><span class="p">(</span><span class="s2">&quot;blueprint_encode&quot;</span><span class="p">,</span> <span class="s2">&quot;2024-02-26&quot;</span><span class="p">,</span> <span class="n">realize_assays</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 <span class="n">immune_cell_ref</span> <span class="o">=</span> <span class="n">celldex</span><span class="o">.</span><span class="n">fetch_reference</span><span class="p">(</span><span class="s2">&quot;dice&quot;</span><span class="p">,</span> <span class="s2">&quot;2024-02-26&quot;</span><span class="p">,</span> <span class="n">realize_assays</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
diff --git a/search.html b/search.html
index dd1b0e8..68187f4 100644
--- a/search.html
+++ b/search.html
@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
 <meta name="robots" content="noindex" />
-<title>Search - singler unknown documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+<title>Search - singler unknown documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
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diff --git a/searchindex.js b/searchindex.js
index 6f4f0d4..d83008e 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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