diff --git a/README.md b/README.md
index 55f4b31..6b3e214 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@
 
 ## Why `cosinor-lite?`
 
-- **Unified workflow for live cell data**: Perform detrending and fit cosinor models with either a fixed 24 h, free-period or damped oscillation with consistent APIs across data modalities (i.e. bioluminescence, cytokines etc.).
+- **Unified workflow for live cell data**: Perform detrending and fit cosinor models with either a fixed 24 h, free-period or damped oscillation with consistent APIs across data modalities (i.e. bioluminescence, cytokines, qPCR etc.).
 - **Differential rhythmicity across any omics type**: Compare two conditions for differential rhythmicity for any type of omics data using BIC model-selection strategies with widespread use in the circadian literature.
 - **Create publication-ready analysis with a simple UI**: Launch a browser-based analysis console for visual quality control, plots, and parameter export.
 
@@ -42,6 +42,8 @@ Here is an adaptation of their figure explaining the methdology:
   <img src="./images/model_selection.png" alt="Model selection" style="width:60%;"/>
 </div>
 
+The tool is very similar to the dryR package in R, but implemented in Python for ease of use with other Python-based data analysis pipelines. Please see the dryR tool for more details, and if you prefer implementing in R (https://github.com/naef-lab/dryR/tree/master).
+
 For condition 1 (i.e. alpha cells) and condition 2 (i.e. beta cells), we fit 5 different models:
 
 - Model 1) Arrhythmic in alpha and beta cells
@@ -68,8 +70,6 @@ uv sync
 source .venv/bin/activate
 ```
 
-> **Tip:** The project targets Python 3.11+. Using `uv` keeps package resolution reproducible via `uv.lock`.
-
 ## Quick Start
 
 ### Launch the interactive app
@@ -102,32 +102,14 @@ fit = analysis.fit(group="treated", model="damped")
 print(fit.parameters)
 ```
 
-## Repository Layout
-
-```
-src/cosinor_lite/        # Core library modules and models
-app.py                   # Gradio application entry point
-tests/                   # Pytest suites (unit, integration, fixtures)
-data/                    # Example datasets for the app
-images/                  # Illustration assets used in the UI
-```
-
-## Development Workflow
-
-```bash
-# run style, type, and security hooks
-pre-commit run --all-files
-
-# execute unit tests
-uv run pytest
-```
 
 ## Sample Datasets
 
 The `data/` directory includes curated examples to help you get started:
 
 - `bioluminescence_example.csv`: Bioluminescence time series for live-cell analysis.
-- `cytokine_example.csv`: An alternative CSV with the same schema for cosinor fitting using cytokine data.
+- `cytokine_example.csv`: Cytokine time series for live-cell analysis.
+- `qpcr_example.csv`: qPCR time series for live-cell analysis.
 - `GSE95156_Alpha_Beta.txt`: RNA-seq data used in the omics differential rhythmicity workflow.
 
 Each file is formatted to drag & drop into `app.py` as well as the library APIs.
diff --git a/app.py b/app.py
index 75a866b..0184d5b 100644
--- a/app.py
+++ b/app.py
@@ -13,7 +13,7 @@
 from cosinor_lite.livecell_cosinor_analysis import CosinorAnalysis
 from cosinor_lite.livecell_dataset import LiveCellDataset
 from cosinor_lite.omics_dataset import OmicsDataset
-from cosinor_lite.omics_differential_rhytmicity import DifferentialRhythmicity, OmicsHeatmap
+from cosinor_lite.omics_differential_rhytmicity import DifferentialRhythmicity, OmicsHeatmap, TimeSeriesExample
 
 plt.rcParams.update(
     {
@@ -29,11 +29,10 @@
 )
 plt.style.use("seaborn-v0_8-ticks")
 
-# --- (your rcParams / styles as-is) ---
-
 APP_DIR = Path(__file__).parent
 bioluminescence_file = str(APP_DIR / "data" / "bioluminescence_example.csv")
 cytokine_file = str(APP_DIR / "data" / "cytokine_example.csv")
+qpcr_file = str(APP_DIR / "data" / "qpcr_example.csv")
 omics_example = str(APP_DIR / "data" / "GSE95156_Alpha_Beta.txt")
 method_img = str(APP_DIR / "images" / "live_cell_fitting-01.png")
 model_selection_img = str(APP_DIR / "images" / "model_selection.png")
@@ -43,11 +42,13 @@
         """
     # Cosinor Analysis App
 
-    A simple app for circadian cosinor analysis & biostatistics.
+    `cosinor-lite`: a simple app for circadian cosinor analysis & biostatistics.
+
+    Choose between the `Live cell` and `Omics` tabs for two different types of analysis:
+    - `Live cell`: inferring rhythmic properties of live cell data using three different cosinor models
+    - `Omics`: differential rhythmicity analysis of omics datasets between two conditions
 
-    Choose between:
-    - inferring rhythmic properties of live cell data using three different cosinor models
-    - differential rhythmicity analysis of omics datasets
+    Developed by the Charna Dibner lab at the Université de Genève and Hôpitaux Universitaires de Genève. See also the associated Python package https://github.com/Nick-E-P/cosinor-lite.
 
     """,
     )
@@ -66,37 +67,51 @@
                 """
             # Fitting live cell data
 
-            This section allows the use to infer parameters describing circadian oscillations in live cell data.
-            Once inferred, the extracted parameters can be compared between groups in downstream analyses. There are three types of cosinor model to choose from:
+            This section allows inference of parameters describing circadian oscillations in live cell data.
+            Once inferred, the extracted parameters can be compared between groups in downstream analyses. Methods are included at the bottom of the page for easy copy-pasting.
+
+            There are three types of cosinor model to choose from:
             - 24h period cosinor
             - Free period (constrained within 20-28h) cosinor
             - Damped cosinor (equivalent to Chronostar analysis), with an additional dampening coefficient
 
-            There are many valid ways to organise the underlying live cell data file. Here we assume a specific format to facilitate data processing
+            ## Input data format
+
+            There are many valid ways to organise the underlying live cell data file. Here we assume a specific format to facilitate data processing.
+            If in doubt, you can download the example files and match the format of your input data accordingly.
 
-            - Row 1: contains a unique identifier for the participant, mouse etc.
+            - Row 1: contains a unique identifier for the participant ID, mouse ID etc.
             - Row 2: replicate number. If there's only one replicate per unique ID, this can just be a row of 1's
-            - Row 3: the group to which each measurement belongs
+            - Row 3: the group to which each measurement belongs (maximum of two groups allowed)
             - Left column; the left column contains the time (going down)
 
+            ## Recommended workflow for examples
+
+            - Bioluminescence: Detrending method: Moving average | Cosinor model: Damped cosinor (Chronostar)
+            - Cytokine: Detrending method: Linear | Cosinor model: Free period cosinor
+            - qPCR: Detrending method: None | Cosinor model: 24h period cosinor
+
             """,
             )
 
             file = gr.File(label="Upload CSV", file_types=[".csv"], type="filepath")
 
             gr.Examples(
-                examples=[bioluminescence_file, cytokine_file],
+                examples=[bioluminescence_file, cytokine_file, qpcr_file],
                 inputs=file,
                 label="Example input",
             )
 
             status = gr.Textbox(label="CSV status", interactive=False)
 
+            gr.Markdown(
+                "Provide the names of your two groups below, as they appear in row 3 of your CSV file.",
+            )
+
             with gr.Row():
                 group1_label = gr.Textbox(label="Group 1 label", value="Group 1")
                 group2_label = gr.Textbox(label="Group 2 label", value="Group 2")
 
-            # State (values will be pandas / numpy objects, not components)
             st_participant_id = gr.State()
             st_replicate = gr.State()
             st_group = gr.State()
@@ -113,7 +128,6 @@ def process_csv(
                 np.ndarray,
                 pd.DataFrame,
             ]:
-                # If needed, normalize FileData dict -> str path here
                 df_data = pd.read_csv(fpath, index_col=0, header=None)
 
                 participant_id = df_data.iloc[0, :].astype(str)
@@ -129,12 +143,9 @@ def process_csv(
 
                 time_rows = df_data.iloc[3:].apply(pd.to_numeric, errors="raise")
 
-                shape_info = (
-                    f"Loaded shape: {df_data.shape} | participants: {len(participant_id)} | time points: {len(time)}"
-                )
+                shape_info = f"Total loaded shape of metadata + data: {df_data.shape} | {len(participant_id)} samples x {len(time)} time points"
                 return shape_info, participant_id, replicate, group, time, time_rows
 
-            # Trigger on both upload and change (Examples sets the value via change)
             for evt in (file.upload, file.change):
                 evt(
                     process_csv,
@@ -175,7 +186,7 @@ def make_plot(  # noqa: PLR0913
                 window: float,
                 m: float,
                 plot_style: str,
-            ) -> tuple[plt.Figure | None, str | None]:
+            ) -> tuple[plt.Figure | None, str | None, str | None]:
                 if (
                     ids_series is None
                     or group_series is None
@@ -183,7 +194,7 @@ def make_plot(  # noqa: PLR0913
                     or time_array is None
                     or time_rows_df is None
                 ):
-                    return None, None
+                    return None, None, None
                 ds = LiveCellDataset(
                     ids=list(ids_series),
                     group=list(group_series),
@@ -194,7 +205,7 @@ def make_plot(  # noqa: PLR0913
                     group2_label=g2,
                 )
                 if method == "moving_average":
-                    fig, pdf_path = ds.plot_group_data(
+                    fig, pdf_path, csv_path = ds.plot_group_data(
                         which_group,
                         method=method,
                         m=int(m),
@@ -202,13 +213,13 @@ def make_plot(  # noqa: PLR0913
                         plot_style=plot_style,
                     )
                 else:
-                    fig, pdf_path = ds.plot_group_data(
+                    fig, pdf_path, csv_path = ds.plot_group_data(
                         which_group,
                         method=method,
                         m=int(m),
                         plot_style=plot_style,
                     )
-                return fig, pdf_path
+                return fig, pdf_path, csv_path
 
             method_choice = gr.Radio(
                 choices=[
@@ -241,6 +252,7 @@ def make_plot(  # noqa: PLR0913
             build_btn = gr.Button("Plot raw data and trend", variant="primary")
             plot = gr.Plot(label="Preview")
             download = gr.File(label="Download plot")
+            detrended_download = gr.File(label="Download detrended CSV")
 
             build_btn.click(
                 make_plot,
@@ -258,7 +270,7 @@ def make_plot(  # noqa: PLR0913
                     m_slider,
                     plot_style_choice,
                 ],
-                outputs=[plot, download],
+                outputs=[plot, download, detrended_download],
             )
 
             cosinor_model = gr.Radio(
@@ -373,15 +385,61 @@ def make_cosinor_fits(  # noqa: PLR0913
                 ],
                 outputs=[plot_cosinor, pdf_export, table_export, download_export],
             )
+            gr.Markdown(
+                """
+            # Fitting Live Cell Data Methods (to paste and adapt as needed)
+
+            Live cell time series from X data were first detrended using:
+
+            - **Linear regression**: ordinary least-squares (statsmodels 0.14.1) was fit to the raw signal versus time, and the fitted mean-centered trend was subtracted to yield detrended residuals.
+            - **Quadratic regression**: a second-order polynomial was fit to the raw signal versus time (NumPy 1.26), and the fitted mean-centered trend was subtracted to yield detrended residuals.
+            - **Centered moving average**: a rolling mean (pandas 2.1.4) with a window of X hours was computed, and detrended values were obtained by subtracting the trend from the raw data.
+
+
+            We extracted periodic parameters from the cell line data by fitting a cosinor model of the form (CHOOSE APPROPRIATE MODEL):
+
+            **24-h cosinor model**
+
+            $$
+            y(t) = \\text{mesor} + \\text{amplitude} \\cdot \\cos\\!\\left(\\frac{2\\pi (t - \\text{acrophase})}{24}\\right),
+            $$
+
+            where $y(t)$ represents the X signal and $t$ represents time in hours. The parameters mesor, amplitude, and acrophase correspond to the mean level, oscillation amplitude, and phase of peak expression, respectively. Model fitting was performed by minimizing the least-squares error using the `curve_fit` function from SciPy (v1.11.4).
+
+            **Free-period cosinor model**
+
+            $$
+            y(t) = \\text{mesor} + \\text{amplitude} \\cdot \\cos\\!\\left(\\frac{2\\pi (t - \\text{acrophase})}{\\text{period}}\\right),
+            $$
+
+            where $y(t)$ represents the X signal and $t$ represents time in hours. The parameters mesor, amplitude, acrophase, and period correspond to the mean level, oscillation amplitude, phase of peak expression, and oscillation period, respectively. Model fitting was performed by minimizing the least-squares error using the `curve_fit` function from SciPy (v1.11.4).
+
+            **Damped cosinor model**
+
+            To account for potential attenuation of oscillatory amplitude over time, we also considered a damped cosinor model with exponential decay,
+
+            $$
+            y(t) = \\text{mesor} + \\text{amplitude} \\cdot e^{-\\lambda t}
+            \\cos\\!\\left(\\frac{2\\pi (t - \\text{acrophase})}{\\text{period}}\\right),
+            $$
+
+            where $y(t)$ represents the X signal and $t$ represents time in hours. The parameters mesor, amplitude, acrophase, and period correspond to the mean level, oscillation amplitude, phase of peak expression, and oscillation period, respectively. The parameter $\\lambda$ is the damping coefficient controlling the rate of exponential decay of the oscillation amplitude. Model fitting was performed by minimizing the least-squares error using the `curve_fit` function from SciPy (v1.11.4).
+
+            """,
+                latex_delimiters=[
+                    {"left": "$$", "right": "$$", "display": True},
+                    {"left": "$", "right": "$", "display": False},
+                ],
+            )
         with gr.Tab("Omics", id=1):
             gr.Markdown(
                 """
-            # Differential rhytmicity analysis of omics datasets
+            # Differential rhythmicity analysis of omics datasets
 
-            Here we perform differential rhythmicity analysis on omics data using a model selection approach.
+            Here we perform differential rhythmicity analysis between two conditions using a model selection approach on omics data.
             The example data includes published RNA-seq data, but in theory any types of omics data (RNA-seq, proteomics, metabolomics, lipidomics) could be used. The dataset is from the following publication:
 
-            Petrenko V, Saini C, Giovannoni L, Gobet C, Sage D, Unser M, Heddad Masson M, Gu G, Bosco D, Gachon F, Philippe J, Dibner C. 2017. Pancreatic alpha- and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression. Genes Dev 31:383-398. doi:10.1101/gad.290379.116.
+            > Petrenko V, Saini C, Giovannoni L, Gobet C, Sage D, Unser M, Heddad Masson M, Gu G, Bosco D, Gachon F, Philippe J, Dibner C. 2017. Pancreatic alpha- and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression. Genes Dev 31:383-398. doi:10.1101/gad.290379.116.
                 """,
             )
 
@@ -390,37 +448,44 @@ def make_cosinor_fits(  # noqa: PLR0913
                 label="Differential rhytmicity analysis with model selection",
                 interactive=False,
                 show_label=True,
-                height=600,  # adjust as needed; or remove to use natural size
+                height=600,
             )
 
             gr.Markdown(
                 """
             ## How does the method actually work?
 
-            The details of the method are nicely explained in the article:
-
-            Pelikan A, Herzel H, Kramer A, Ananthasubramaniam B. 2022. Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. The FEBS Journal 289:6605-6621. doi:10.1111/febs.16095
+            Methods are included at the bottom of the page for easy copy-pasting. The details of the method are nicely explained in the article:
+            > Pelikan A, Herzel H, Kramer A, Ananthasubramaniam B. 2022. Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. The FEBS Journal 289:6605–6621. doi:10.1111/febs.16095
 
             See the above adaptation of their figure explaining the methodology.
 
-            For condition 1 (i.e. alpha cells) and condition 2 (i.e. beta cells), we fit five different models:
+            The tool is very similar to the dryR package in R, but implemented in Python for ease of use with other Python-based data analysis pipelines. Please see the dryR tool for more details, and if you prefer implementing in R.
+            https://github.com/naef-lab/dryR/tree/master
 
-            - Model 1) Arrhythmic in alpha and beta cells
-            - Model 2) Rhythmic in beta cells only
-            - Model 3) Rhythmic in alpha cells only
-            - Model 4) Rhythmic in alpha and beta cells with the same rhythmic parameters (i.e. phase and amplitude)
-            - Model 5) Rhythmic in both but with differential rhythmicity in alpha vs beta cells
+            ### Model selection approach
+
+            For condition 1 (i.e. cell type 1) and condition 2 (i.e. cell type 2), we fit five different models:
+
+            - Model 1) Arrhythmic in cell type 1 and cell type 2
+            - Model 2) Rhythmic in cell type 2 only
+            - Model 3) Rhythmic in cell type 1 only
+            - Model 4) Rhythmic in cell type 1 and cell type 2 with the same rhythmic parameters (i.e. phase and amplitude)
+            - Model 5) Rhythmic in both but with differential rhythmicity in cell type 1 vs cell type 2
 
             A degree of confidence is calculated for each model (called model weight, which sums to 1 across all models), and a model is chosen if the model weight exceeds a threshold (for this tutorial we will use 0.5). If no model exceeds this threshold, then the model is unclassified, which we define as Model 0.
 
             - Model 0) unclassified
 
+            ### Note for data input
+
+            The input file needs a "Genes" column, followed by columns containing expression values for each sample. See the example file for reference.
+
                 """,
             )
 
-            # File input + example
             omics_file = gr.File(
-                label="Upload Omics TXT/TSV",
+                label="Upload Omics CSV/TXT/TSV",
                 file_types=[".txt", ".tsv", ".csv"],
                 type="filepath",
             )
@@ -432,7 +497,6 @@ def make_cosinor_fits(  # noqa: PLR0913
 
             omics_status = gr.Textbox(label="File status", interactive=False)
 
-            # Multiselects for choosing columns by header names
             columns_cond1_dd = gr.Dropdown(
                 choices=[],
                 multiselect=True,
@@ -444,22 +508,24 @@ def make_cosinor_fits(  # noqa: PLR0913
                 label="Condition B columns (e.g., ZT_*_b_*)",
             )
 
-            # Optional manual time vectors
             override_time = gr.Checkbox(
-                label="Override time vectors manually?",
+                label="Provide time points manually (i.e. the time associated with each sample)?",
                 value=False,
             )
             t_cond1_tb = gr.Textbox(label="t_cond1 (comma-separated)", visible=False)
             t_cond2_tb = gr.Textbox(label="t_cond2 (comma-separated)", visible=False)
+            log2_choice = gr.Radio(
+                choices=[("No", "no"), ("Yes", "yes")],
+                value="no",
+                label="Apply log2 transform to expression data?",
+            )
 
-            # Hidden state to stash the DataFrame
             st_df_rna = gr.State()
+            st_rhythmic = gr.State()
 
-            # Preview planned inputs for your class
             omics_preview = gr.Code(label="Planned class inputs", language="python")
             build_omics_btn = gr.Button("Build Omics inputs", variant="primary")
 
-            # Sample dropdowns for replicate scatterplot
             sample1_dd = gr.Dropdown(choices=[], label="Sample 1 (x-axis)")
             sample2_dd = gr.Dropdown(choices=[], label="Sample 2 (y-axis)")
             scatter_btn = gr.Button(
@@ -469,29 +535,19 @@ def make_cosinor_fits(  # noqa: PLR0913
             scatter_plot = gr.Plot(label="Replicate scatterplot")
             scatter_download = gr.File(label="Download scatterplot")
 
-            # Histogram outputs
             hist_btn = gr.Button("Generate histogram", variant="primary")
             omics_plot = gr.Plot(label="Expression histogram")
             omics_download = gr.File(label="Download histogram")
 
-            # ---------- helpers ----------
             def _guess_cols(cols: Sequence[str]) -> tuple[list[str], list[str]]:
                 cols = [str(c) for c in cols]
                 a_guess = [c for c in cols if re.search(r"_a_", str(c))]
                 b_guess = [c for c in cols if re.search(r"_b_", str(c))]
-
-                def zt_key(col: str) -> int:
-                    m = re.search(r"ZT_(\d+)", str(col))
-                    return int(m.group(1)) if m else 0
-
-                a_guess = sorted(a_guess, key=zt_key)
-                b_guess = sorted(b_guess, key=zt_key)
                 return a_guess, b_guess
 
             def _pick_default_samples(
                 cols: Sequence[str],
             ) -> tuple[str | None, str | None]:
-                # Try ZT_0 ... _1 and ZT_0 ... _2 as a sensible default pair
                 s1 = next((c for c in cols if re.search(r"ZT_0_.*_1$", str(c))), None)
                 s2 = next((c for c in cols if re.search(r"ZT_0_.*_2$", str(c))), None)
                 if s1 and s2 and s1 != s2:
@@ -509,16 +565,17 @@ def _build_time_vec(n_cols: int, manual_text: str | None) -> list[float]:
                 reps = max(1, (n_cols + len(base) - 1) // len(base))
                 return [float(value) for value in (base * reps)[:n_cols]]
 
-            # ---------- loaders & toggles ----------
             def load_omics(
                 fpath: str | Path,
             ) -> tuple[object, object, object, pd.DataFrame, object, object, object, object]:
-                # Read TSV (tab-separated). Pandas also handles CSV if present.
-                dataframe = pd.read_csv(fpath, sep="\t")
-                # Drop first column by index (your pipeline)
-                if dataframe.shape[1] > 0:
-                    dataframe = dataframe.drop(dataframe.columns[0], axis=1)
-                # Create Genes column from gene_name if present
+                fpath_str = str(fpath)
+                if fpath_str.endswith((".txt", ".tsv")):
+                    dataframe = pd.read_csv(fpath, sep="\t", index_col=None)
+                elif fpath_str.endswith(".csv"):
+                    dataframe = pd.read_csv(fpath, index_col=None)
+                else:
+                    dataframe = pd.read_csv(fpath, index_col=None)
+
                 if "gene_name" in dataframe.columns:
                     dataframe["Genes"] = dataframe["gene_name"].astype(str).str.split("|").str[1]
 
@@ -565,7 +622,6 @@ def toggle_time_fields(checked: object) -> tuple[object, object]:
                 outputs=[t_cond1_tb, t_cond2_tb],
             )
 
-            # ---------- preview inputs for your future class ----------
             def build_omics_inputs(  # noqa: PLR0913
                 df: pd.DataFrame | None,
                 cols_a: Sequence[str] | None,
@@ -591,21 +647,11 @@ def build_omics_inputs(  # noqa: PLR0913
                     t_b_text if manual_flag else None,
                 )
 
-                snippet = f"""# Planned inputs for your Omics class
+                snippet = f"""# Planned inputs for the Omics dataset class
         columns_cond1 = {cols_a}
         columns_cond2 = {cols_b}
         t_cond1 = {t_a}
         t_cond2 = {t_b}
-
-        # Example construction (later):
-        # rna_data = OmicsDataset(
-        #     df=df_rna,
-        #     columns_cond1=columns_cond1,
-        #     columns_cond2=columns_cond2,
-        #     t_cond1=t_cond1,
-        #     t_cond2=t_cond2,
-        #     deduplicate_on_init=True,
-        # )
         """
                 return snippet
 
@@ -622,7 +668,6 @@ def build_omics_inputs(  # noqa: PLR0913
                 outputs=omics_preview,
             )
 
-            # ---------- histogram ----------
             def run_histogram(  # noqa: PLR0913
                 df: pd.DataFrame | None,
                 cols_a: Sequence[str] | None,
@@ -630,6 +675,7 @@ def run_histogram(  # noqa: PLR0913
                 use_manual_time: object,
                 t_a_text: str | None,
                 t_b_text: str | None,
+                log2_option: str,
             ) -> tuple[plt.Figure | None, str | None]:
                 if df is None:
                     return None, None
@@ -643,6 +689,7 @@ def run_histogram(  # noqa: PLR0913
 
                 t_a_array = np.asarray(t_a, dtype=float)
                 t_b_array = np.asarray(t_b, dtype=float)
+                apply_log2 = log2_option == "yes"
 
                 rna_data = OmicsDataset(
                     df=df,
@@ -651,6 +698,7 @@ def run_histogram(  # noqa: PLR0913
                     t_cond1=t_a_array,
                     t_cond2=t_b_array,
                     deduplicate_on_init=True,
+                    log2_transform=apply_log2,
                 )
 
                 fig = rna_data.expression_histogram()
@@ -670,11 +718,11 @@ def run_histogram(  # noqa: PLR0913
                     override_time,
                     t_cond1_tb,
                     t_cond2_tb,
+                    log2_choice,
                 ],
                 outputs=[omics_plot, omics_download],
             )
 
-            # ---------- replicate scatterplot ----------
             def run_replicate_scatter(  # noqa: PLR0913
                 df: pd.DataFrame | None,
                 cols_a: Sequence[str] | None,
@@ -684,6 +732,7 @@ def run_replicate_scatter(  # noqa: PLR0913
                 t_b_text: str | None,
                 sample1: str | None,
                 sample2: str | None,
+                log2_option: str,
             ) -> tuple[plt.Figure | None, str | None]:
                 if df is None or not sample1 or not sample2:
                     return None, None
@@ -697,6 +746,7 @@ def run_replicate_scatter(  # noqa: PLR0913
 
                 t_a_array = np.asarray(t_a, dtype=float)
                 t_b_array = np.asarray(t_b, dtype=float)
+                apply_log2 = log2_option == "yes"
 
                 rna_data = OmicsDataset(
                     df=df,
@@ -705,6 +755,7 @@ def run_replicate_scatter(  # noqa: PLR0913
                     t_cond1=t_a_array,
                     t_cond2=t_b_array,
                     deduplicate_on_init=True,
+                    log2_transform=apply_log2,
                 )
 
                 fig = rna_data.replicate_scatterplot(sample1=sample1, sample2=sample2)
@@ -726,17 +777,13 @@ def run_replicate_scatter(  # noqa: PLR0913
                     t_cond2_tb,
                     sample1_dd,
                     sample2_dd,
+                    log2_choice,
                 ],
                 outputs=[scatter_plot, scatter_download],
             )
-
-            # ------------------------------------------------------------
-            # Differential rhythmicity + heatmap
-            # (Paste this inside your existing `with gr.Tab("Omics", id=1):` block)
-            # Re-uses helpers: _build_time_vec, and states/components you already created.
-            # ------------------------------------------------------------
-
-            # Labels for the heatmap and expressed-threshold
+            gr.Markdown(
+                "Define a cutoff for expressed genes, based on mean expression or number of detected samples.",
+            )
             with gr.Row():
                 cond1_label_tb = gr.Textbox(
                     label="Condition 1 label",
@@ -751,13 +798,17 @@ def run_replicate_scatter(  # noqa: PLR0913
                     value=0,
                     precision=0,
                 )
+                num_detected_num = gr.Number(
+                    label="num_detected_min (for is_expressed)",
+                    value=0,
+                    precision=0,
+                )
 
             compute_dr_btn = gr.Button(
                 "Compute differential rhythmicity & heatmap",
                 variant="primary",
             )
 
-            # Outputs
             heatmap_plot = gr.Plot(label="Heatmap preview")
             heatmap_download = gr.File(label="Download heatmap (PDF)")
             params_preview = gr.Dataframe(
@@ -776,23 +827,23 @@ def run_dr_and_heatmap(  # noqa: PLR0913
                 cond1_label: str,
                 cond2_label: str,
                 mean_min: float | None,
-            ) -> tuple[plt.Figure | None, str | None, pd.DataFrame | None, str | None]:
+                num_detected_min: float | None,
+                log2_option: str,
+            ) -> tuple[plt.Figure | None, str | None, pd.DataFrame | None, str | None, pd.DataFrame | None]:
                 if df is None or not cols_a or not cols_b:
-                    # Nothing to do yet
-                    return None, None, None, None
+                    return None, None, None, None, None
 
                 cols_a = list(cols_a or [])
                 cols_b = list(cols_b or [])
                 manual_flag = bool(use_manual_time)
 
-                # Build time vectors (reuse your helper)
                 t_a = _build_time_vec(len(cols_a), t_a_text if manual_flag else None)
                 t_b = _build_time_vec(len(cols_b), t_b_text if manual_flag else None)
 
                 t_a_array = np.asarray(t_a, dtype=float)
                 t_b_array = np.asarray(t_b, dtype=float)
+                apply_log2 = log2_option == "yes"
 
-                # Construct dataset
                 rna_data = OmicsDataset(
                     df=df,
                     columns_cond1=cols_a,
@@ -800,20 +851,22 @@ def run_dr_and_heatmap(  # noqa: PLR0913
                     t_cond1=t_a_array,
                     t_cond2=t_b_array,
                     deduplicate_on_init=True,
+                    log2_transform=apply_log2,
                 )
 
-                # Mark expressed genes
                 try:
                     mean_min_value = float(mean_min) if mean_min is not None else 0.0
                 except (TypeError, ValueError):
                     mean_min_value = 0.0
-                rna_data.add_is_expressed(mean_min=mean_min_value)
+                try:
+                    num_detected_value = int(num_detected_min) if num_detected_min is not None else None
+                except (TypeError, ValueError):
+                    num_detected_value = None
+                rna_data.add_is_expressed(mean_min=mean_min_value, num_detected_min=num_detected_value)
 
-                # Differential rhythmicity
                 dr = DifferentialRhythmicity(dataset=rna_data)
                 rhythmic_all = dr.extract_all_circadian_params()  # pandas DataFrame
 
-                # Build heatmap
                 heatmap = OmicsHeatmap(
                     df=rhythmic_all,
                     columns_cond1=cols_a,
@@ -826,22 +879,17 @@ def run_dr_and_heatmap(  # noqa: PLR0913
                 )
                 fig = heatmap.plot_heatmap()  # should return a Matplotlib Figure
 
-                # Save outputs for download
-
-                # Heatmap PDF
                 with tempfile.NamedTemporaryFile(delete=False, suffix=".pdf") as tmp_pdf:
                     fig.savefig(tmp_pdf.name)
                     tmp_pdf_path = tmp_pdf.name
 
-                # Rhythmic params CSV
                 with tempfile.NamedTemporaryFile(delete=False, suffix=".csv") as tmp_csv:
                     rhythmic_all.to_csv(tmp_csv.name, index=False)
                     tmp_csv_path = tmp_csv.name
 
-                # For preview table, show up to 200 rows to keep UI snappy
                 preview_df = rhythmic_all.head(20)
 
-                return fig, tmp_pdf_path, preview_df, tmp_csv_path
+                return fig, tmp_pdf_path, preview_df, tmp_csv_path, rhythmic_all
 
             compute_dr_btn.click(
                 run_dr_and_heatmap,
@@ -855,12 +903,138 @@ def run_dr_and_heatmap(  # noqa: PLR0913
                     cond1_label_tb,
                     cond2_label_tb,
                     mean_min_num,
+                    num_detected_num,
+                    log2_choice,
                 ],
                 outputs=[
                     heatmap_plot,
                     heatmap_download,
                     params_preview,
                     params_download,
+                    st_rhythmic,
+                ],
+            )
+            gr.Markdown("## Visualise an individual gene")
+            gr.Markdown("Note that no model will be shown if the gene was not classified confidently.")
+            gene_text = gr.Textbox(label="Gene symbol", placeholder="e.g., Arntl")
+            gene_btn = gr.Button("Plot gene time series", variant="secondary")
+            gene_plot = gr.Plot(label="Gene time series")
+            gene_download = gr.File(label="Download gene plot")
+
+            def plot_gene_time_series(  # noqa: PLR0913
+                rhythmic_df: pd.DataFrame | None,
+                gene_symbol: str,
+                cols_a: Sequence[str] | None,
+                cols_b: Sequence[str] | None,
+                use_manual_time: object,
+                t_a_text: str | None,
+                t_b_text: str | None,
+                cond1_label: str,
+                cond2_label: str,
+            ) -> tuple[plt.Figure | None, str | None]:
+                if rhythmic_df is None or rhythmic_df.empty:
+                    msg = "Run the differential rhythmicity analysis first."
+                    raise ValueError(msg)
+                if not gene_symbol or not gene_symbol.strip():
+                    msg = "Enter a gene symbol to plot."
+                    raise ValueError(msg)
+
+                cols_a = list(cols_a or [])
+                cols_b = list(cols_b or [])
+                if not cols_a or not cols_b:
+                    msg = "Select columns for both conditions."
+                    raise ValueError(msg)
+
+                manual_flag = bool(use_manual_time)
+                t_a = _build_time_vec(len(cols_a), t_a_text if manual_flag else None)
+                t_b = _build_time_vec(len(cols_b), t_b_text if manual_flag else None)
+
+                t_a_array = np.asarray(t_a, dtype=float)
+                t_b_array = np.asarray(t_b, dtype=float)
+
+                example = TimeSeriesExample(
+                    df=rhythmic_df,
+                    columns_cond1=cols_a,
+                    columns_cond2=cols_b,
+                    t_cond1=t_a_array,
+                    t_cond2=t_b_array,
+                    cond1_label=cond1_label or "Condition 1",
+                    cond2_label=cond2_label or "Condition 2",
+                )
+                fig = example.plot_time_series(gene_symbol.strip(), show=False)
+
+                with tempfile.NamedTemporaryFile(delete=False, suffix=".pdf") as tmp_pdf:
+                    fig.savefig(tmp_pdf.name)
+                    pdf_path = tmp_pdf.name
+                plt.close(fig)
+                return fig, pdf_path
+
+            gene_btn.click(
+                plot_gene_time_series,
+                inputs=[
+                    st_rhythmic,
+                    gene_text,
+                    columns_cond1_dd,
+                    columns_cond2_dd,
+                    override_time,
+                    t_cond1_tb,
+                    t_cond2_tb,
+                    cond1_label_tb,
+                    cond2_label_tb,
+                ],
+                outputs=[gene_plot, gene_download],
+            )
+            gr.Markdown(
+                """
+            ## Differential Rhythmicity Analysis Methods (to paste and adapt as needed)
+
+            Differential rhythmicity analysis was performed using harmonic linear regression and model selection based on the Bayesian Information Criterion (BIC) (Atger et al., 2015, Pelikan et al., 2022).
+
+            We used the harmonic linear regression model
+
+            $$
+            y(t) = m + a \\cos(\\omega t) + b \\sin(\\omega t),
+            $$
+
+            where $y(t)$ represents the log2-transformed values of either transcript or protein levels, $m$ is the mean level, $\\omega$ is the frequency of the oscillations (fixed to give a period of 24 h), $t$ is the time, and $a$ and $b$ are the regression coefficients of the cosine and sine terms, respectively.
+
+            We proposed five different models to represent different rhythmic categories. Model $M_1$ corresponds to arrhythmic behavior in both Condition 1 and Condition 2 cells. Model $M_2$ corresponds to rhythmicity in Condition 2 cells only, whereas model $M_3$ corresponds to rhythmicity in Condition 1 cells only. Model $M_4$ corresponds to rhythmicity in both Condition 1 and Condition 2 cells with identical rhythmic parameters (i.e. identical coefficients $a$ and $b$). Model $M_5$ corresponds to rhythmicity in both cell types with differential rhythmicity between Condition 1 and Condition 2 cells (i.e. different coefficients $a$ and $b$).
+
+            For each model $M_i$, the regression was performed and the BIC was calculated as
+
+            $$
+            \\mathrm{BIC}_i = k_i \\ln(n) - 2 \\ln(\\hat{L}_i),
+            $$
+
+            where $k_i$ is the number of parameters in model $M_i$, $n$ is the sample size, and $\\hat{L}_i$ is the maximized value of the likelihood function for model $M_i$.
+
+            For model comparison, the difference between the BIC of each model and the lowest BIC value among all models (denoted $\\mathrm{BIC}_{\\min}$) was computed as
+
+            $$
+            \\Delta_i = \\mathrm{BIC}_i - \\mathrm{BIC}_{\\min}.
+            $$
+
+            The Schwarz weight $w_i$ of each model was then calculated as
+
+            $$
+            w_i = \\frac{\\exp\\left(-\\tfrac{1}{2}\\Delta_i\\right)}{\\sum_i \\exp\\left(-\\tfrac{1}{2}\\Delta_i\\right)}.
+            $$
+
+            Genes were considered as detected if the mean log2 RPKM level was ≥ X, and proteins were considered as detected if at least Y out of Z samples had a detectable level. Detected status was denoted using several subclasses: subclass $a$, detected in Condition 1 cells only; subclass $b$, detected in Condition 2 cells only; and subclass $c$, detected in both Condition 1 and Condition 2 cells.
+
+            For each model there is an associated set of possible subclasses: model $M_1$ allows subclasses $a$, $b$, and $c$; model $M_2$ allows subclasses $b$ and $c$; model $M_3$ allows subclasses $a$ and $c$; model $M_4$ allows subclass $c$ only; model $M_5$ allows subclass $c$ only; and model $M_0$ allows subclass $c$ only.
+
+            To generate lists of oscillatory genes or proteins, we summed the model weights corresponding to rhythmic expression for the condition of interest. If this summed weight exceeded the Schwarz weight cutoff of 0.5, the feature was classified as oscillatory. For example, for Condition 1 cells, oscillatory features were those supported by models $M_3$, $M_4$, and $M_5$.
+
+            **References**
+
+            > Atger F, Gobet C, Marquis J, Martin E, Wang J, Weger B, Lefebvre G, Descombes P, Naef F, Gachon F. 2015. Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver. Proceedings of the National Academy of Sciences 112:E6579–E6588. doi:10.1073/pnas.1515308112
+
+            > Pelikan A, Herzel H, Kramer A, Ananthasubramaniam B. 2022. Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. The FEBS Journal 289:6605–6621. doi:10.1111/febs.16095
+            """,
+                latex_delimiters=[
+                    {"left": "$$", "right": "$$", "display": True},
+                    {"left": "$", "right": "$", "display": False},
                 ],
             )
 
diff --git a/data/GSE95156_Alpha_Beta.csv b/data/GSE95156_Alpha_Beta.csv
new file mode 100644
index 0000000..490e481
--- /dev/null
+++ b/data/GSE95156_Alpha_Beta.csv
@@ -0,0 +1,14028 @@
+Genes,ZT_0_a_1,ZT_4_a_1,ZT_8_a_1,ZT_12_a_1,ZT_16_a_1,ZT_20_a_1,ZT_0_a_2,ZT_4_a_2,ZT_8_a_2,ZT_12_a_2,ZT_16_a_2,ZT_20_a_2,ZT_0_b_1,ZT_4_b_1,ZT_8_b_1,ZT_12_b_1,ZT_16_b_1,ZT_20_b_1,ZT_0_b_2,ZT_4_b_2,ZT_8_b_2,ZT_12_b_2,ZT_16_b_2,ZT_20_b_2
+Gnai3,5.21257288664975,4.97433680974948,5.18439042243561,5.11141506683397,4.72619558289174,4.90900320377913,4.67050834523666,4.96904990783596,5.18558475348983,5.0627812821099,4.78194839591953,4.91548826855172,6.02077015156944,5.45470432619129,5.82523181475896,5.74584475793277,5.48914272853758,5.85046213617587,5.29828493601712,5.70435150533922,5.69832274365148,5.50367675122733,5.4235104017499,5.54802077946833
+Cdc45,0.184519394812012,0.512578434302474,0.182007369408326,0.66807010455708,0.323858442157409,0.321661292851492,0.261030927277802,-0.437269632287699,0.592482781988891,0.0133858372073543,0.559252131068257,-0.0652017618021949,0.819789385638511,0.561282350703038,0.541903907379743,0.294699024560891,0.931832842615669,0.591007894069664,0.803632594702474,0.485963966401581,1.18609398089446,0.938563263959061,0.955716611211992,0.696273133077087
+Scml2,-2.18574128766452,-1.56208675059526,-1.43586353278925,-1.05881895282545,-2.46700430913977,-1.79885410540941,-1.08771732349223,-1.86989682365411,-1.06009252454032,-1.41924135415906,-2.10876746631793,-2.26750590136763,-3.27808059355473,-2.29651891687164,-3.65155340071635,-2.71125070682457,-2.81758472385108,-2.69202178529737,-2.62251124281439,-2.50426666654887,-1.70030738112015,-2.3982938308816,-3.95003318465993,-3.04930949594164
+Narf,1.3798424798799,1.8500916570151,1.55795485314043,2.13259262854345,1.5558364972157,1.16426348871046,1.40360541763726,2.11052225317104,1.79521305114007,2.12600394914109,1.62840821783015,1.82386726736609,1.49946904692935,1.8523125517143,1.60810788961086,2.00340667759805,1.78002581478088,1.32320768284098,1.7493894414463,1.89230686598551,1.70539606112513,1.75324905323557,1.78736272349504,2.03771954430567
+Cav2,2.5730697603149,2.02768908605418,2.09552915629973,1.62172031878828,1.94746842013256,2.25452632757688,2.04523870330071,2.44695821238335,2.44822157668416,1.5030686240726,1.71571561306825,2.10476762879395,-3.462129404961,-1.67032015136136,-1.41028729956819,-2.92490082902526,-2.120561349384,-1.99936416796083,-2.36478185601474,-2.16696573976946,-2.27814719089344,-2.79011506195478,-2.75893464814112,-1.3882266310465
+Klf6,3.45052755317535,3.92419940080187,2.96958632525943,3.42643774618294,3.44393251441376,3.25190169585205,3.06007738011164,3.22679199686806,4.67318247594152,3.42688921913147,3.46655927425982,3.53742623359347,2.98828290120308,2.86490141996643,2.3816294107304,2.92315222702633,2.66317223916545,3.03294856413769,2.72770136779904,3.00926617847123,3.33950619121033,2.95448703729902,3.0395483642056,2.96392740595873
+Scmh1,1.57962331040779,1.85560955487359,1.93410159818831,1.5660023398482,2.41342424263999,2.57879197969704,2.12126940790305,2.23718983073347,1.78287788915067,1.86483901018183,2.33725017374482,1.93506118091017,1.61870220495618,1.68409197169127,1.51979037716061,1.51412855012253,2.31759916822578,1.94265664737031,2.31897726573636,1.64618510383373,1.68406226442009,1.57336549916379,2.13587612326563,1.84227409720804
+Cox5a,2.86412798280212,2.17099315916554,2.65628458196535,2.73995423852567,2.38567319865963,2.36727736819482,2.39163994065855,1.77290940090742,2.78487786074305,2.59828484816663,2.29428075932595,2.66423517467467,4.42667872093675,3.74680990225155,4.19677684022746,3.74012882663465,4.09175776010394,4.17106273033875,3.878060077512,4.17229712400695,3.99796100833238,3.5894100323968,3.90264529780137,3.628166802118
+Wnt9a,-1.07445246263388,-1.12522600957192,-3.05760839064152,-2.45473165692201,-1.59825916083339,-1.514850314138,-1.61987677395046,-0.85010562613462,-1.17435221636264,-1.13366483216283,-2.05342685669244,-1.04041491739353,-2.68227031767142,-1.66772226042967,-1.93726088597099,-2.56792435442991,-2.30957918008361,-3.46635804867177,-2.63947684499869,-2.16436784883777,-3.08696943604839,-2.52592835590483,-3.50137829685505,-2.68282420468274
+Fer,2.5783470558356,2.54409991614559,2.56227689437104,2.66749846632705,2.78836480118853,3.00838276685555,2.82848354729497,2.52720998783662,2.62346304976729,2.59465818688886,2.9119462124926,2.59746713690314,3.10060375149211,3.05776608910531,3.0861309517684,3.16405542822872,2.88539465825404,3.03906014893335,3.11476863315555,2.97870965987139,3.01609042292402,3.05931497160821,3.05237391652703,2.92180046321939
+Xpo6,2.53862844930509,2.81089832929782,2.39113849560221,2.73962660684193,3.15639805253471,3.2294066911843,3.06773675995538,2.43562644290909,2.60245642936183,2.53515706956956,3.10603818794571,2.82838441761589,2.30416230061411,2.55308166760272,2.39701225248966,2.57753819011324,2.99891912003699,2.71531792957745,3.09286630380301,2.21422711299259,2.19230810488467,2.35032774941965,2.94269156295404,2.79380151958307
+Tfe3,2.23691992665498,2.26134725038941,2.20772786875758,2.25693643503227,2.53009306073133,2.60087783222744,2.39349837807574,2.39613957075211,2.29120897394093,2.24923921156251,2.43521235908308,2.27937065318909,1.79148621622192,1.86985901192119,1.56351165217702,1.82629924985702,1.99133846571604,1.89353555059168,2.16455699698237,1.68550754346153,1.90574357145025,1.8237602872103,1.93729828646817,1.88923213878654
+Axin2,1.96136344552499,2.07766391583331,1.98399671832236,1.83661016902198,1.9274650484208,2.06238721071578,2.01892739594965,2.35229858261109,2.19982478320383,2.06955625754926,2.07609715931281,2.01723823745374,0.787335612978814,1.43848991223447,0.841937144560321,1.15250587737013,1.1703128699124,1.08786252992825,1.23465960089924,1.34677666128258,0.847110029942101,0.793567571998347,1.36882035016422,1.00262079134518
+Baat1,1.89268705925366,2.14180097692119,2.05892525984495,2.06073517130217,2.06208591039638,1.97305529060852,2.03919250309341,1.92771671836064,1.98395139952956,2.05644269559712,1.86413234132662,2.16875759553323,1.59489858232944,1.9512420814664,1.70495319636702,2.14554556054997,1.97143874078467,1.86945250360989,1.90025647636098,2.01449927286771,2.03006634610123,2.15463374237028,1.84856791805016,2.07872575234159
+Gna12,4.31685197439924,4.0722930211003,4.36209257950553,4.17222958552504,4.05227591633601,4.19422270313622,3.93050240502269,4.1821976205975,4.32268359551859,4.06497302177396,4.12843653601751,4.0049896168959,3.76945505249837,3.79995396899633,3.95901466165163,3.87235564874572,4.10256752120301,4.0869577645581,3.87333880669834,3.87365985719779,3.81091809327304,3.92459471499942,4.01242725875374,3.86610776737802
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+Plscr1,3.29300180843864,3.17532317673523,3.55576325667236,3.28153988225277,2.94658227256744,3.01549078953857,2.96368186177195,3.4689583909114,3.23764016942089,3.28074595651974,3.3816763317287,3.35243658087136,3.65116774701845,3.65642338293186,3.71171584662143,3.53671956836702,3.08995820149216,3.31355096278039,3.3341805195688,3.79835991336642,3.64014819562571,3.86961495322322,3.37739133017026,3.13614345643366
+Lactb,2.4209301334875,1.99482542624442,2.0836970580091,2.26587471861625,1.55937039115994,1.91630384083187,1.76419494202224,1.31673110566978,2.026963223997,2.09834597346326,1.99407489466716,1.60009749945996,2.67161236878244,2.53365321770988,2.20284271478943,2.94139559665608,2.35642495580265,2.37471664585406,2.33833387303239,2.33935233576259,2.57760452328959,2.51398160242034,2.23100197969319,2.37802492155819
+Plod2,0.283656590159172,0.534554476702033,0.580477362748896,0.229263836539465,-0.478317336411908,0.186327134337804,-0.321213671019702,0.516287737723613,0.410983750863192,0.178460596452337,-0.189181169875114,0.473212830329897,-0.895235108561728,-0.102717325876187,-0.267630001434797,-0.662568482185368,-2.27690846372684,-0.659300113010348,-2.96754573318084,-0.621914190978351,-0.548891794642072,-0.315681082585813,-1.81434168243949,-1.71369762829696
+Aph1b,2.14671460979453,2.19429150211841,2.08114878568595,2.02355889079318,1.92156238773878,1.69271398233199,1.77274636691092,2.15843753108917,1.95091020778047,2.11083510789016,1.9395614778522,2.0675765604456,2.04899986297391,1.70085940575694,2.25673356208258,2.0560670096671,1.83444696794986,1.9003384494941,1.35587803857803,2.0771903751251,2.01029786009913,1.9768647928534,1.76791130052885,2.09123236244165
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+AC102862.2,-1.02396260527884,-1.84980220134483,-1.47703398274752,-1.06179134428911,0.212590298366462,-0.155890479206788,-0.373016360650645,-0.977822978667637,-0.898887862196447,-0.88321633347949,-0.654697841732746,-1.26806043152729,-4.54442088718318,-4.54442088718318,-4.54442088718318,-4.54442088718318,-2.97852143409114,-4.54442088718318,-3.88284991951075,-4.54442088718318,-4.54442088718318,-4.54442088718318,-4.54442088718318,-3.90776908515327
+AC113320.1,0.878108143196212,0.840308358337375,0.865324888243794,0.804207657453983,0.693250664743321,0.361278635941499,0.0150625563782529,0.749079186954835,1.21216155436077,0.858818718391532,0.776141652419452,0.938583331934211,1.29583018615777,0.680952689785251,1.13765458610946,1.34730101513967,0.689328637852024,1.41528416773642,0.465387962600775,1.65094327754643,0.734430508139808,0.695990248644726,0.995333954301999,1.17418439222729
+AC121960.1,-3.54179201182388,-3.50451709764141,-4.04667825693777,-3.53663181023964,-2.31333267378705,-2.04965969891437,-2.87979970468355,-3.48923233255378,-3.54972157594104,-4.04667825693777,-2.82160857155295,-3.50336028644234,0.652518048953123,0.799698440820166,0.463730479591857,0.943753215692784,2.6043946479437,1.81037127812304,2.55320010432983,0.286034808688432,0.644004784991833,0.687375678808229,2.24058268713783,2.26102471200047
diff --git a/data/qpcr_example.csv b/data/qpcr_example.csv
new file mode 100644
index 0000000..5c5f5ce
--- /dev/null
+++ b/data/qpcr_example.csv
@@ -0,0 +1,10 @@
+Participant ID,1,1,2,2,3,3,4,5,5,6,6,7,7,8,8,9,10,11
+Replicate,1,2,1,2,1,2,1,1,2,1,2,1,2,1,2,1,1,1
+Group,Group 1,Group 1,Group 1,Group 1,Group 1,Group 1,Group 1,Group 1,Group 1,Group 2,Group 2,Group 2,Group 2,Group 2,Group 2,Group 2,Group 1,Group 2
+12,0.1521,0.1157,0.2137,0.2373,,0.1287,0.2434,0.3844,0.5509,0.1456,0.1192,0.2279,0.2544,0.1478,0.165,0.2433,0.0757,0.169
+16,0.2682,0.235,0.522,0.5362,0.2034,0.1663,0.5834,0.7298,0.5026,0.1357,0.1508,0.357,0.3393,0.2616,0.2432,0.2816,0.1228,0.2285
+20,0.2328,0.2364,0.7227,0.6,0.2074,0.1887,0.6815,0.6507,0.7113,0.1493,0.1641,0.4117,,0.3647,0.2158,0.2677,0.1582,0.2619
+24,0.1691,0.1394,0.4334,0.4078,0.1752,0.2141,0.4122,0.5008,0.5088,0.1237,0.1432,0.3894,,0.2779,0.2997,0.2772,0.1534,0.3343
+28,0.078,0.065,0.1708,0.1662,0.1165,0.145,0.1788,0.2429,0.2548,0.0888,0.0764,0.1327,0.1392,0.1387,0.103,0.1846,0.0791,
+32,0.0546,0.062,0.1118,0.111,0.1157,0.088,0.1201,0.1236,0.115,0.0656,0.0867,0.1163,0.1133,0.0948,0.1096,0.1236,0.0582,0.1021
+36 ,0.0784,0.0719,0.1551,0.1334,0.1091,0.1146,0.1724,0.1765,0.2084,0.1214,,0.1048,0.1442,0.2728,0.2212,0.2097,0.072,0.1603
diff --git a/notebooks/live_cell_tutorial.ipynb b/notebooks/live_cell_tutorial.ipynb
index ae805fa..841ae47 100644
--- a/notebooks/live_cell_tutorial.ipynb
+++ b/notebooks/live_cell_tutorial.ipynb
@@ -113,7 +113,8 @@
     "- poly2 (linear + quadratic terms)\n",
     "- moving_average (need to provide number of window steps)\n",
     "\n",
-    "As measurements are every 10 mins, we'll use a moving_average window of 240 (24 hour moving average window)."
+    "As measurements are every 10 mins, we'll use a moving_average window of 240 (24 hour moving average window).\n",
+    "The helper returns a matplotlib figure along with temporary PDF and CSV paths so you can download both the plot and the detrended traces."
    ]
   },
   {
@@ -123,7 +124,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, tmp_path = dataset.plot_group_data(\"group1\", method=\"moving_average\", window=240, plot_style=\"line\")"
+    "fig, tmp_path, csv_path = dataset.plot_group_data(\n",
+    "    \"group1\",\n",
+    "    method=\"moving_average\",\n",
+    "    window=240,\n",
+    "    plot_style=\"line\",\n",
+    ")"
    ]
   },
   {
diff --git a/notebooks/omics_tutorial.ipynb b/notebooks/omics_tutorial.ipynb
index 6739159..9a006e3 100644
--- a/notebooks/omics_tutorial.ipynb
+++ b/notebooks/omics_tutorial.ipynb
@@ -72,8 +72,9 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "from cosinor_lite.datasets import OmicsDataset\n",
-    "from cosinor_lite.differential_rhytmicity_omics import DifferentialRhythmicity, OmicsHeatmap, TimeSeriesExample\n",
+    "\n",
+    "from cosinor_lite.omics_dataset import OmicsDataset\n",
+    "from cosinor_lite.omics_differential_rhytmicity import DifferentialRhythmicity, OmicsHeatmap, TimeSeriesExample\n",
     "\n",
     "plt.rcParams.update(\n",
     "    {\n",
@@ -210,8 +211,9 @@
     "    t_cond1=t_cond1,\n",
     "    t_cond2=t_cond2,\n",
     "    deduplicate_on_init=True,\n",
+    "    log2_transform=False,\n",
     ")\n",
-    "rna_data.expression_histogram()"
+    "fig = rna_data.expression_histogram()"
    ]
   },
   {
@@ -231,7 +233,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "rna_data.replicate_scatterplot(sample1=\"ZT_0_a_1\", sample2=\"ZT_0_a_2\")"
+    "fig = rna_data.replicate_scatterplot(sample1=\"ZT_0_a_1\", sample2=\"ZT_0_a_2\")"
    ]
   },
   {
@@ -239,7 +241,7 @@
    "id": "13",
    "metadata": {},
    "source": [
-    "In some cases this may reveal that measurements below a certain threshold look visually less correlated between samples. Here we will defines genes as non-expressed using the threshold of <0, as used in the original 2017 article."
+    "In some cases this may reveal that measurements below a certain threshold look visually less correlated between samples. Here we will defines genes as non-expressed using a mean expression cut-off of 0 and requiring at least two detected measurements per condition, matching the original 2017 article."
    ]
   },
   {
@@ -249,7 +251,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "rna_data.add_is_expressed(mean_min=0)"
+    "rna_data.add_is_expressed(mean_min=0, num_detected_min=2)"
    ]
   },
   {
@@ -302,7 +304,7 @@
     "    cond2_label=\"Beta cells\",\n",
     "    show_unexpressed=False,\n",
     ")\n",
-    "heatmap.plot_heatmap()"
+    "fig = heatmap.plot_heatmap()"
    ]
   },
   {
@@ -332,12 +334,16 @@
     "    cond2_label=\"Beta cells\",\n",
     ")\n",
     "\n",
-    "# example.plot_time_series(\"Scg2\", xticks=np.arange(0, 25, 4))\n",
-    "# example.plot_time_series(\"Upk3a\", xticks=np.arange(0, 25, 4))\n",
-    "# example.plot_time_series(\"Kcnk3\", xticks=np.arange(0, 25, 4))\n",
-    "\n",
-    "example.plot_time_series(\"Ntrk1\", xticks=np.arange(0, 25, 4))"
+    "example.plot_time_series(\"Arntl\", xticks=np.arange(0, 25, 4))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
diff --git a/run.sh b/run.sh
index 85ca410..ab49125 100755
--- a/run.sh
+++ b/run.sh
@@ -26,7 +26,7 @@ function test:quick {
 
 # execute tests against the installed package; assumes the wheel is already installed
 function test:ci {
-    INSTALLED_PKG_DIR="$(python -c 'import cosinor_lite; print(cosinor_lite.__path__[0])')"
+    INSTALLED_PKG_DIR="$(uv run python -c 'import cosinor_lite; print(cosinor_lite.__path__[0])')"
     # in CI, we must calculate the coverage for the installed package, not the src/ folder
     COVERAGE_DIR="$INSTALLED_PKG_DIR" run-tests
 }
@@ -47,7 +47,7 @@ function run-tests {
 }
 
 function serve-coverage-report {
-    python -m http.server 8000 \
+    uv run python -m http.server 8000 \
         --bind 127.0.0.1 \
         --directory "$THIS_DIR/test-reports/htmlcov/"
 }
diff --git a/src/cosinor_lite/livecell_dataset.py b/src/cosinor_lite/livecell_dataset.py
index 45bcbb5..8a0b537 100644
--- a/src/cosinor_lite/livecell_dataset.py
+++ b/src/cosinor_lite/livecell_dataset.py
@@ -50,7 +50,7 @@ class LiveCellDataset:
         poly2_trend(x, y): Fits a second-order polynomial trend to the data.
         moving_average_trend(x, y, window): Computes a moving average trend.
         get_trend(x, y, method, window): Applies the specified detrending method.
-        plot_group_data(group, method, window, m, plot_style): Plots time series data for the specified group.
+        plot_group_data(group, method, window, m, plot_style): Plots time series data for the specified group and exports detrended values.
 
     """
 
@@ -247,7 +247,7 @@ def moving_average_trend(
         y_series = pd.Series(y)
         ma_fit = y_series.rolling(window=window, center=True).mean().to_numpy()
         good = np.isfinite(x) & np.isfinite(ma_fit)
-        y_detrended = y[good] - ma_fit[good] + np.mean(y[good])
+        y_detrended = y[good] - ma_fit[good]  # + np.mean(y[good])
         return x[good], ma_fit[good], y_detrended
 
     def get_trend(
@@ -301,14 +301,14 @@ def get_trend(
         msg = f"Unknown detrending method: {method}"
         raise ValueError(msg)
 
-    def plot_group_data(
+    def plot_group_data(  # noqa: PLR0915
         self,
         group: str,
         method: str = "linear",
         window: int = 5,
         m: int = 5,
         plot_style: str = "scatter",
-    ) -> tuple[plt.Figure, str]:
+    ) -> tuple[plt.Figure, str, str]:
         """
         Plots data for a specified group, with options for trend fitting and plot style.
 
@@ -332,6 +332,8 @@ def plot_group_data(
             The matplotlib Figure object containing the plots.
         tmp_path : str
             The path to the saved temporary PDF file of the figure.
+        csv_path : str
+            The path to a temporary CSV containing detrended data in input-like layout.
 
         Raises
         ------
@@ -340,32 +342,39 @@ def plot_group_data(
 
         """
         if group == "group1":
-            ids, _replicates, data = self.get_group1_ids_replicates_data()
+            ids, replicates, data = self.get_group1_ids_replicates_data()
             color = self.color_group1
             group_label = self.group1_label
         elif group == "group2":
-            ids, _replicates, data = self.get_group2_ids_replicates_data()
+            ids, replicates, data = self.get_group2_ids_replicates_data()
             color = self.color_group2
             group_label = self.group2_label
         else:
             msg = "group must be 'group1' or 'group2'"
             raise ValueError(msg)
 
-        n_group = len(np.unique(ids))
+        ids_array = np.array(ids)
+        replicates_array = np.array(replicates)
+        n_group = len(np.unique(ids_array))
         n_cols = m
         n_rows = int(np.ceil(n_group / n_cols))
 
-        study_list = np.unique(ids).tolist()
+        study_list = np.unique(ids_array).tolist()
         fig = plt.figure(figsize=(5 * n_cols / 2.54, 5 * n_rows / 2.54))
 
+        detrended_matrix = np.full_like(data, np.nan, dtype=float)
+
         for i, id_curr in enumerate(study_list):
-            mask = np.array(ids) == id_curr
+            mask = ids_array == id_curr
             n_reps = int(np.sum(mask))
             ax = fig.add_subplot(n_rows, n_cols, i + 1)
 
+            col_indices = np.where(mask)[0]
+
             for j in range(n_reps):
                 x = self.time
-                y = data[:, mask][:, j]
+                col_idx = col_indices[j]
+                y = data[:, col_idx]
 
                 if plot_style == "scatter":
                     ax.scatter(x, y, s=4, alpha=0.8, color=color)
@@ -376,12 +385,18 @@ def plot_group_data(
                 x_fit = x[valid_mask]
                 y_fit = y[valid_mask]
 
-                x_processed, trend, _y_detrended = self.get_trend(
+                x_processed, trend, y_detrended = self.get_trend(
                     x_fit,
                     y_fit,
                     method=method,
                     window=window,
                 )
+                detrended_full = np.full_like(x, np.nan, dtype=float)
+                for x_val, y_val in zip(x_processed, y_detrended, strict=False):
+                    idx_candidates = np.where(np.isclose(x, x_val))[0]
+                    if idx_candidates.size:
+                        detrended_full[idx_candidates[0]] = y_val
+                detrended_matrix[:, col_idx] = detrended_full
                 if method != "none":
                     ax.plot(
                         x_processed,
@@ -403,4 +418,23 @@ def plot_group_data(
 
         fig.savefig(tmp_path)
 
-        return fig, tmp_path
+        csv_fd, csv_path = tempfile.mkstemp(suffix=".csv")
+        os.close(csv_fd)
+
+        column_labels = [f"col_{i + 1}" for i in range(detrended_matrix.shape[1])]
+        table_rows = [
+            np.array(ids_array, dtype=object),
+            np.array(replicates_array, dtype=object),
+            np.array([group_label] * detrended_matrix.shape[1], dtype=object),
+        ]
+        table_rows.extend(detrended_matrix.astype(object))
+        index_labels = [
+            "participant_id",
+            "replicate",
+            "group",
+            *[float(t) for t in self.time],
+        ]
+        export_df = pd.DataFrame(table_rows, index=index_labels, columns=column_labels)
+        export_df.to_csv(csv_path, index=True, header=False, na_rep="")
+
+        return fig, tmp_path, csv_path
diff --git a/src/cosinor_lite/omics_dataset.py b/src/cosinor_lite/omics_dataset.py
index 57d6aa7..24be69c 100644
--- a/src/cosinor_lite/omics_dataset.py
+++ b/src/cosinor_lite/omics_dataset.py
@@ -47,6 +47,8 @@ class OmicsDataset:
         Display label for condition 2, by default ``"cond2"``.
     deduplicate_on_init : bool, optional
         Whether to deduplicate genes immediately after initialization, by default ``False``.
+    log2_transform : bool, optional
+        Whether to apply a log2(x + 1) transform to expression columns on init, by default ``False``.
 
     """
 
@@ -60,6 +62,7 @@ class OmicsDataset:
     cond2_label: str = "cond2"
 
     deduplicate_on_init: bool = False
+    log2_transform: bool = False
 
     @field_validator("t_cond1", "t_cond2", mode="before")
     @classmethod
@@ -115,12 +118,21 @@ def _check_columns(self) -> Self:
 
     def __post_init__(self) -> None:
         """Populate derived columns and optionally deduplicate entries."""
+        if self.log2_transform:
+            self._apply_log2_transform()
         self.add_detected_timepoint_counts()
         self.add_mean_expression()
         self.add_number_detected()
         if self.deduplicate_on_init:
             self.deduplicate_genes()
 
+    def _apply_log2_transform(self) -> None:
+        """Apply a log2(x + 1) transform to measurement columns."""
+        measurement_cols = self.columns_cond1 + self.columns_cond2
+        numeric = self.df[measurement_cols].apply(pd.to_numeric, errors="coerce")
+        transformed = np.log2(numeric + 1.0)
+        self.df.loc[:, measurement_cols] = transformed
+
     def detected_timepoint_counts(self, cond: str) -> list[int]:
         """
         Count detected time points per gene for the requested condition.
@@ -165,8 +177,8 @@ def add_detected_timepoint_counts(self) -> None:
 
     def add_mean_expression(self) -> None:
         """Compute mean expression for both conditions and store in the DataFrame."""
-        self.df["mean_cond1"] = self.df[self.columns_cond1].mean(axis=1)
-        self.df["mean_cond2"] = self.df[self.columns_cond2].mean(axis=1)
+        self.df["mean_cond1"] = self.df[self.columns_cond1].mean(axis=1, skipna=True)
+        self.df["mean_cond2"] = self.df[self.columns_cond2].mean(axis=1, skipna=True)
 
     def add_number_detected(self) -> None:
         """Store the count of non-null measurements for each condition."""
@@ -247,7 +259,7 @@ def expression_histogram(self, bins: int = 20) -> plt.Figure:
 
         """
         print(plt.rcParams["font.size"])
-        fig = plt.figure(figsize=(6 / 2.54, 12 / 2.54))
+        fig = plt.figure(figsize=(8 / 2.54, 12 / 2.54))
         plt.subplot(2, 1, 1)
         plt.hist(self.df["mean_cond1"].to_numpy().flatten(), bins=bins)
         plt.xlabel("Mean Expression")
diff --git a/src/cosinor_lite/omics_differential_rhytmicity.py b/src/cosinor_lite/omics_differential_rhytmicity.py
index 1cba7b8..8f4f5dc 100644
--- a/src/cosinor_lite/omics_differential_rhytmicity.py
+++ b/src/cosinor_lite/omics_differential_rhytmicity.py
@@ -588,7 +588,6 @@ def rhythmic_genes_expressed_cond1(self) -> pd.DataFrame:
         mask: pd.Series = (df["is_expressed_cond1"]) & ~(df["is_expressed_cond2"])
         df_to_analyse: pd.DataFrame = df[mask].reset_index(drop=True)
 
-        model_ids: list[int] = [model.name for model in MODELS_ONE_CONDITION]
         rows: list[dict] = []
         for gene, row in tqdm(
             df_to_analyse.set_index("Genes").iterrows(),
@@ -604,20 +603,18 @@ def rhythmic_genes_expressed_cond1(self) -> pd.DataFrame:
             if float(np.nanmax(weights)) < self.BIC_cutoff:
                 best_result = M0()
                 chosen_model_biw: float = np.nan
-                model: int = 0
+                chosen_model: int = 0
             else:
                 pick: int = int(np.nanargmax(weights))
                 best_result = results[pick]
                 chosen_model_biw = float(weights[pick])
-                model = int(best_result.name)
-            weight_columns = _weight_mapping(model_ids, weights)
+                chosen_model = [1, 3][pick]
             rows.append(
                 {
                     "gene": gene,
-                    "model": model,
+                    "model": chosen_model,
                     "chosen_model_bicw": chosen_model_biw,
-                    # "weight": weights[pick],
-                    **weight_columns,
+                    **{f"w_model{model_id}": weights[i] for i, model_id in enumerate([1, 3])},
                     "alpha_phase": getattr(best_result, "phase", np.nan),
                     "alpha_amp": getattr(best_result, "amp", np.nan),
                     "beta_phase": np.nan,
@@ -644,7 +641,6 @@ def rhythmic_genes_expressed_cond2(self) -> pd.DataFrame:
         mask: pd.Series = ~(df["is_expressed_cond1"]) & (df["is_expressed_cond2"])
         df_to_analyse: pd.DataFrame = df[mask].reset_index(drop=True)
 
-        model_ids: list[int] = [model.name for model in MODELS_ONE_CONDITION]
         rows: list[dict] = []
         for gene, row in tqdm(
             df_to_analyse.set_index("Genes").iterrows(),
@@ -660,20 +656,18 @@ def rhythmic_genes_expressed_cond2(self) -> pd.DataFrame:
             if float(np.nanmax(weights)) < self.BIC_cutoff:
                 best_result = M0()
                 chosen_model_biw: float = np.nan
-                model: int = 0
+                chosen_model: int = 0
             else:
                 pick: int = int(np.nanargmax(weights))
                 best_result = results[pick]
                 chosen_model_biw = float(weights[pick])
-                model = int(best_result.name)
-            weight_columns = _weight_mapping(model_ids, weights)
+                chosen_model = [1, 2][pick]
             rows.append(
                 {
                     "gene": gene,
-                    "model": model,
+                    "model": chosen_model,
                     "chosen_model_bicw": chosen_model_biw,
-                    # "weight": weights[pick],
-                    **weight_columns,
+                    **{f"w_model{model_id}": weights[i] for i, model_id in enumerate([1, 2])},
                     "alpha_phase": np.nan,
                     "alpha_amp": np.nan,
                     "beta_phase": getattr(best_result, "phase", np.nan),
@@ -852,7 +846,6 @@ def timepoint_means(
 
         Raises
         ------
-        ValueError
             If the number of columns differs from the number of time labels provided.
 
         """
@@ -860,14 +853,17 @@ def timepoint_means(
             text: str = f"Length of columns ({len(columns)}) must match length of times ({len(times)})"
             raise ValueError(text)
 
-        values: np.ndarray = df[columns].to_numpy()
-        unique_times: np.ndarray = np.unique(times)
+        values: np.ndarray = df[columns].apply(pd.to_numeric, errors="coerce").to_numpy(dtype=float)
 
-        result: np.ndarray = np.column_stack(
-            [values[:, times == t].mean(axis=1) for t in unique_times],
-        )
+        times_arr: np.ndarray = np.asarray(times)
+        unique_times: np.ndarray = pd.unique(times_arr)
 
-        return result
+        with np.errstate(all="ignore"):
+            means: np.ndarray = np.column_stack(
+                [np.nanmean(values[:, times_arr == t], axis=1) for t in unique_times],
+            )
+
+        return means
 
     def get_z_score(self, arr: np.ndarray) -> np.ndarray:
         """
@@ -884,10 +880,25 @@ def get_z_score(self, arr: np.ndarray) -> np.ndarray:
             Z-score normalized matrix preserving the original shape.
 
         """
-        means: np.ndarray = np.mean(arr, axis=1, keepdims=True)
-        stds: np.ndarray = np.std(arr, axis=1, keepdims=True)
-        safe_stds: np.ndarray = np.where(stds == 0, 1, stds)
-        return (arr - means) / safe_stds
+        a: np.ndarray = np.asarray(arr, dtype=float)
+
+        row_all_nan: np.ndarray = np.asarray(
+            np.isnan(a).all(axis=1, keepdims=True),
+            dtype=bool,
+        )
+
+        mu: np.ndarray = np.nanmean(a, axis=1, keepdims=True)
+        sd: np.ndarray = np.nanstd(a, axis=1, ddof=0, keepdims=True)
+
+        sd = np.where(sd == 0.0, 1.0, sd)
+
+        mu = np.where(row_all_nan, 0.0, mu)
+        sd = np.where(row_all_nan, 1.0, sd)
+
+        z: np.ndarray = (a - mu) / sd
+        z = np.where(row_all_nan, np.nan, z)
+
+        return z
 
     def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
         """
@@ -970,7 +981,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[0, 0].set_title("Alpha cells")
@@ -997,7 +1008,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
         axes[1, 0].set_xticks([])
         axes[1, 0].set_yticks([])
@@ -1021,7 +1032,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
         axes[2, 0].set_xticks([])
         axes[2, 0].set_yticks([])
@@ -1045,7 +1056,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
         axes[3, 0].set_xticks([])
         axes[3, 0].set_yticks([])
@@ -1070,7 +1081,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
         axes[4, 0].set_xticks([])
         axes[4, 0].set_yticks([])
@@ -1095,7 +1106,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[5, 0].set_xticks(range(len(t_unique)), t_unique)
@@ -1122,7 +1133,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[0, 1].set_title("Beta cells")
@@ -1138,7 +1149,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[1, 1].set_xticks([])
@@ -1155,7 +1166,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[2, 1].set_xticks([])
@@ -1170,7 +1181,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[3, 1].set_xticks([])
@@ -1185,7 +1196,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[4, 1].set_xticks([])
@@ -1200,7 +1211,7 @@ def plot_heatmap(self, cmap: str = "bwr") -> plt.Figure:  # noqa: PLR0915
             vmin=vmin_global,
             vmax=vmax_global,
             rasterized=False,
-            interpolation="none",
+            interpolation="nearest",
         )
 
         axes[5, 1].set_xticks(range(len(t_unique)), t_unique)
@@ -1297,7 +1308,13 @@ def _check_columns(self) -> Self:
             raise ValueError(text)
         return self
 
-    def plot_time_series(self, gene: str, xticks: np.ndarray | None = None) -> None:
+    def plot_time_series(
+        self,
+        gene: str,
+        xticks: np.ndarray | None = None,
+        *,
+        show: bool = True,
+    ) -> plt.Figure:
         """
         Visualize observed expression values with corresponding model fits.
 
@@ -1307,6 +1324,8 @@ def plot_time_series(self, gene: str, xticks: np.ndarray | None = None) -> None:
             Gene identifier to visualize.
         xticks : numpy.ndarray | None, optional
             Custom x-axis tick positions, by default ``None`` for automatic values.
+        show : bool, optional
+            Whether to display the figure immediately, by default ``True``.
 
         Raises
         ------
@@ -1352,28 +1371,33 @@ def plot_time_series(self, gene: str, xticks: np.ndarray | None = None) -> None:
                 self.t_cond2,
                 model,
             )
-        plt.figure(figsize=(12 / 2.54, 6 / 2.54))
-        plt.subplot(1, 2, 1)
-        plt.scatter(self.t_cond1, alpha_vec, s=4)
-        plt.plot(t_test, y_test_cond1)
-        plt.ylabel("Expression Level")
-        plt.xticks(xticks)
-
-        plt.title(f"Time Series for {gene}")
-        plt.xlabel("Time (h)")
-        plt.subplot(1, 2, 2)
-        plt.scatter(self.t_cond2, beta_vec, s=4, color="r")
-        plt.plot(t_test, y_test_cond2, color="r")
-        plt.title(f"Time Series for {gene}")
-        plt.xlabel("Time (h)")
-
-        plt.xticks(xticks)
-        plt.xlim(
-            xticks[0] - 0.05 * (xticks[-1] - xticks[0]),
-            xticks[-1] + 0.05 * (xticks[-1] - xticks[0]),
-        )
-        plt.tight_layout()
-        plt.show()
+        fig, axes = plt.subplots(1, 2, figsize=(12 / 2.54, 6 / 2.54))
+        ax_alpha, ax_beta = axes
+
+        ax_alpha.scatter(self.t_cond1, alpha_vec, s=4)
+        ax_alpha.plot(t_test, y_test_cond1)
+        ax_alpha.set_ylabel("Expression Level")
+        ax_alpha.set_xticks(xticks)
+        ax_alpha.set_title(f"{gene}- {self.cond1_label}")
+        ax_alpha.set_xlabel("Time (h)")
+
+        ax_beta.scatter(self.t_cond2, beta_vec, s=4, color="r")
+        ax_beta.plot(t_test, y_test_cond2, color="r")
+        ax_beta.set_title(f"{gene}: {self.cond2_label}")
+        ax_beta.set_xlabel("Time (h)")
+        ax_beta.set_xticks(xticks)
+
+        for ax in axes:
+            ax.set_xlim(
+                xticks[0] - 0.05 * (xticks[-1] - xticks[0]),
+                xticks[-1] + 0.05 * (xticks[-1] - xticks[0]),
+            )
+
+        fig.tight_layout()
+        if show:
+            fig.show()
+
+        return fig
 
     def get_test_function_expressed_both(
         self,
diff --git a/tests/unit_tests/test_livecell_dataset.py b/tests/unit_tests/test_livecell_dataset.py
index 2ffb67a..108c957 100644
--- a/tests/unit_tests/test_livecell_dataset.py
+++ b/tests/unit_tests/test_livecell_dataset.py
@@ -141,9 +141,14 @@ def test_get_trend_invalid_method(bioluminescence_dataset: LiveCellDataset) -> N
 
 @pytest.mark.parametrize("group", ["group1", "group2"])
 def test_plot_group_data(bioluminescence_dataset: LiveCellDataset, group: str) -> None:
-    fig, tmp_path = bioluminescence_dataset.plot_group_data(group=group, method="linear", plot_style="scatter")
+    fig, tmp_path, csv_path = bioluminescence_dataset.plot_group_data(
+        group=group,
+        method="linear",
+        plot_style="scatter",
+    )
     assert hasattr(fig, "savefig")  # noqa: S101
     assert tmp_path.endswith(".pdf")  # noqa: S101
+    assert csv_path.endswith(".csv")  # noqa: S101
 
 
 def test_plot_group_data_invalid_group(bioluminescence_dataset: LiveCellDataset) -> None:
diff --git a/tests/unit_tests/test_omics_dataset.py b/tests/unit_tests/test_omics_dataset.py
index c28e7a5..52926c1 100644
--- a/tests/unit_tests/test_omics_dataset.py
+++ b/tests/unit_tests/test_omics_dataset.py
@@ -83,3 +83,43 @@ def test_replicate_scatterplot_title_matches_correlations(omics_dataset: OmicsDa
         assert figure.axes[0].get_title() == expected_title  # noqa: S101
     finally:
         plt.close(figure)
+
+
+def test_log2_transform_applies_to_measurements(omics_dataset: OmicsDataset) -> None:
+    dataset = omics_dataset
+    measurement_cols = dataset.columns_cond1 + dataset.columns_cond2
+    transformed = OmicsDataset(
+        df=dataset.df.copy(),
+        columns_cond1=list(dataset.columns_cond1),
+        columns_cond2=list(dataset.columns_cond2),
+        t_cond1=dataset.t_cond1.copy(),
+        t_cond2=dataset.t_cond2.copy(),
+        cond1_label=dataset.cond1_label,
+        cond2_label=dataset.cond2_label,
+        log2_transform=True,
+    )
+
+    expected = np.log2(dataset.df[measurement_cols].astype(float) + 1.0)
+    actual = transformed.df[measurement_cols]
+
+    assert np.allclose(actual.to_numpy(), expected.to_numpy(), equal_nan=True)  # noqa: S101
+
+
+def test_add_is_expressed_respects_num_detected_min(omics_dataset: OmicsDataset) -> None:
+    dataset = omics_dataset
+    # Force known counts by zeroing some entries
+    df_copy = dataset.df.copy()
+    cond1_cols = dataset.columns_cond1
+    df_copy.loc[:, cond1_cols] = np.nan
+    df_copy.loc[:, cond1_cols[:1]] = 10.0
+
+    test_ds = OmicsDataset(
+        df=df_copy,
+        columns_cond1=list(dataset.columns_cond1),
+        columns_cond2=list(dataset.columns_cond2),
+        t_cond1=dataset.t_cond1.copy(),
+        t_cond2=dataset.t_cond2.copy(),
+    )
+    test_ds.add_is_expressed(num_detected_min=2)
+
+    assert not test_ds.df["is_expressed_cond1"].any()  # noqa: S101
diff --git a/tests/unit_tests/test_omics_differential_rhytmicity.py b/tests/unit_tests/test_omics_differential_rhytmicity.py
index b0f0623..096eb11 100644
--- a/tests/unit_tests/test_omics_differential_rhytmicity.py
+++ b/tests/unit_tests/test_omics_differential_rhytmicity.py
@@ -327,3 +327,10 @@ def test_time_series_example_conditional_predictions(time_series_example: TimeSe
 def test_time_series_example_plot_time_series_missing_gene(time_series_example: TimeSeriesExample) -> None:
     with pytest.raises(ValueError, match="not found"):
         time_series_example.plot_time_series("missing_gene")
+
+
+def test_time_series_example_plot_time_series_returns_figure(time_series_example: TimeSeriesExample) -> None:
+    fig = time_series_example.plot_time_series("gene_both", show=False)
+
+    assert isinstance(fig, plt.Figure)  # noqa: S101
+    plt.close(fig)