Update download URL link

docs/notebooks/01_prepare_data.ipynb

@@ -12,7 +12,7 @@
     "* Corresponding reference genome sequence in fasta format (and corresponding index)\n",
     "* Aligned LRTS data in bam format (and corresponding index)\n",
     "\n",
-    "In this tutorial, we provide guidelines about how to prepare aligned LRTS read files (.bam) and the reference genome and annotation data. **Subsequent tutorials on IsoTools workflow do not depend on executing these steps**. We have compiled a small pre-processed demonstration data set, based on a subset of the genome ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)). Below, we document how this example data set was produced. \n",
+    "In this tutorial, we provide guidelines about how to prepare aligned LRTS read files (.bam) and the reference genome and annotation data. **Subsequent tutorials on IsoTools workflow do not depend on executing these steps**. We have compiled a small pre-processed demonstration data set, based on a subset of the genome ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)). Below, we document how this example data set was produced. \n",
     "\n",
     "In order to prepare the files for IsoTools analysis, the following tools are needed:\n",
     "\n",

docs/notebooks/02_api_vs_cli.ipynb

@@ -12,7 +12,7 @@
     "All command line parameters are described in the [CLI section](../isotoolsCLI.html):\n",
     "\n",
     "\n",
-    "To run the commands, need the following **input files** from the [prepared demonstration dataset](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd):\n",
+    "To run the commands, need the following **input files** from the [prepared demonstration dataset](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8):\n",
     "\n",
     "* sample description file 'encode_samples.tsv'\n",
     "* six .bam alignment files for the six samples\n",

docs/notebooks/03_transcriptome_reconstruction.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Transcriptome Reconstruction\n",
     "This tutorial processes the example data set, based on PacBio Isoseq samples of hematopoetic cells from ENCODE. This dataset contains only a subset of genomic regions, allowing for fast processing of the demonstration tutorials. \n",
-    "All required data files to run the tutorials can be obtained here: ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)). \n",
+    "All required data files to run the tutorials can be obtained here: ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)). \n",
     "\n",
     "To run this example, you will you will need the following **input files**:\n",
     "\n",

docs/notebooks/03b_transcriptome_import.ipynb

@@ -11,7 +11,7 @@
     "\n",
     "The transcriptome gtf should contain a transcript entry for each transcript with long read coverage, but may also contain additional transcripts for reference. The transcript table contains one row per transcript, with transcript id, and a column for each sample specifying the number of long reads. \n",
     "All additional tags from the gtf info field get imported, and can be used within isotools for subsequent analysis. \n",
-    "All files used in the tutorial can be obtained here: ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)). \n",
+    "All files used in the tutorial can be obtained here: ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)). \n",
     "\n",
     "\n",
     "You will need:\n",

docs/notebooks/04_saturation_analysis.ipynb

@@ -17,7 +17,7 @@
     "    * If the curve is relatively flat towards the right, deeper sequencing would yield little additional transcripts.\n",
     "    * Can be restricted to a subset of transcripts (e.g. only matching reference annotation or only novel genes)\n",
     "    \n",
-    "The following steps assume you have run the [previous tutorial](03_transcriptome_reconstruction.html), and prepared a transcriptome pkl file PacBio_isotools.pkl based on the [demonstration dataset](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)."
+    "The following steps assume you have run the [previous tutorial](03_transcriptome_reconstruction.html), and prepared a transcriptome pkl file PacBio_isotools.pkl based on the [demonstration dataset](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)."
    ]
   },
   {

docs/notebooks/05_qc.ipynb

@@ -19,7 +19,7 @@
     "\n",
     "We will quantify these artifacts using [filter_stats](../isotoolsAPI.html?highlight=filter_stats#isotools.Transcriptome.filter_stats), which returns a table with the number of reads affected per sample or group of samples.\n",
     "The fraction of affected reads can be visualized as bars, plot using [plot_bar](../isotoolsAPI.html?highlight=plot_bar#isotools.plots.plot_bar) function.\n",
-    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)."
+    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)."
    ]
   },
   {

docs/notebooks/06_filtering.ipynb

@@ -17,7 +17,7 @@
     "* define custom tags and filter expressions, to tailor filter queries.\n",
     "\n",
     "\n",
-    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)."
+    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)."
    ]
   },
   {

docs/notebooks/08_alternative_splicing.ipynb

@@ -22,7 +22,7 @@
     "In this tutorial, we learn to use ASE to calculate 2D embeddings (PCA, UMAP), representing the relation of the samples with respect to alternative splicing. \n",
     "This representation may be a useful as a first step of the analysis, to validate hypothesis and check sample integrity. \n",
     "\n",
-    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)."
+    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)."
    ]
   },
   {

docs/notebooks/09_diff_splice.ipynb

@@ -12,7 +12,7 @@
     "\n",
     "In this tutorial, we will apply the statistical test to find differential splicing between K562 and GM12878 (on chromosome 8), and how to interpret and depict the results. \n",
     "\n",
-    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)."
+    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)."
    ]
   },
   {

docs/notebooks/10_domains.ipynb

@@ -15,7 +15,7 @@
     "\n",
     "In this tutorial we learn how to use the different resources to functionally annotate the identified transcript isoforms, to depict the domain structure, and to integrate the domain information with differential splicing analysis. \n",
     "\n",
-    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd). Since domains depend on ORF predictions, make sure you ran the [add_orf_prediction()](../isotoolsAPI.html?highlight=add_orf_prediction#isotools.Transcriptome.add_orf_prediction) function during transcriptome reconstruction. "
+    "This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file \"PacBio_isotools.pkl\" based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8). Since domains depend on ORF predictions, make sure you ran the [add_orf_prediction()](../isotoolsAPI.html?highlight=add_orf_prediction#isotools.Transcriptome.add_orf_prediction) function during transcriptome reconstruction. "
    ]
   },
   {