Update case study notebooks and overview images

README.md

@@ -64,7 +64,7 @@ transcriptome.save('../tests/data/example_1_isotools.pkl')
 
 ## Citation and feedback
 
-* If you run into any issues, please use the [github issues report feature](https://github.com/HerwigLab/IsoTools2/issues).
+* If you run into any issues, please use the [github issues](https://github.com/HerwigLab/IsoTools2/issues) report feature.
 * For general feedback, please write us an email to [yalan_bi@molgen.mpg.de](mailto:yalan_bi@molgen.mpg.de) and [herwig@molgen.mpg.de](mailto:herwig@molgen.mpg.de).
 * If you use IsoTools in your publication, please cite the following paper in addition to this repository:
   * Lienhard, Matthias et al. “**IsoTools: a flexible workflow for long-read transcriptome sequencing analysis**.” Bioinformatics (Oxford, England) vol. 39,6 (2023): btad364. [doi:10.1093/bioinformatics/btad364](https://doi.org/10.1093/bioinformatics/btad364)

docs/notebooks/ENCODE_S2.ipynb

@@ -9,8 +9,20 @@
     "This tutorial guides through a typical Long Read Transcriptome Sequencing (LRTS) analysis workflow with isotools, \n",
     "using ENCODE Isoseq Sequel2 Data. It demonstrates the analysis of alternative splicing events within and between sample groups. \n",
     "\n",
-    "The original analysis integrates quite a large number of samples, and consequently runs several hours. Users interested in reproducing the notebook should consider restricting the data to the samples they are interested in.\n",
-    "\n",
+    "The original analysis integrates quite a large number of samples, and consequently runs several hours. Users interested in reproducing the notebook should consider restricting the data to the samples they are interested in."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Note:** This case study was analysed with the old version 0.2.7 of IsoTools and has not been updated to reflect the current API and output conventions."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "## Preparation\n",
     "In this notebook, \"long read RNA-seq\" samples are downloaded from ENCODE to the \"encode\" subdirectory. You can also manually download the files using the data portal (https://www.encodeproject.org/) and download aligned .bam files. Here I use all Sequel II samples leukemia and b-cell samples the time of writing, but you can choose to process a subset. \n",
     "\n",

docs/notebooks/isotools_alzheimer.ipynb

@@ -6,8 +6,20 @@
    "source": [
     "# Case Study: PacBio 2019 Alzheimer Sequel2 dataset\n",
     "\n",
-    "This notebook demonstrates the data preprocessing, import and basic vizualization of genes with Sashimi plots. As it is based on a full sized isoseq dataset, it involves some preparation, and takes several hours to complete. For a smaller example, please check the test data notebook on the [github page](https://github.com/MatthiasLienhard/isotools/blob/master/notebooks/test_data.ipynb).\n",
-    "\n",
+    "This notebook demonstrates the data preprocessing, import and basic vizualization of genes with Sashimi plots. As it is based on a full sized isoseq dataset, it involves some preparation, and takes several hours to complete. For a smaller example, please check the test data notebook on the [github page](https://github.com/MatthiasLienhard/isotools/blob/master/notebooks/test_data.ipynb)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Note:** This case study was analysed with the old version 0.2.8 of IsoTools and has not been updated to reflect the current API and output conventions."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "## Preparation\n",
     "1) Prepare the working directory and download the reference and data\n",
     "``` bash\n",
@@ -46,7 +58,8 @@
     "    ref='reference/GRCh38.p13.genome.fa'\n",
     "    pbmm2 align ${ref} alzheimer/flnc/${sample}_flnc.bam alzheimer/aligned/${sample}_aligned.sorted.bam --preset ISOSEQ --sort -j $n_threads \n",
     "```\n",
-    "\n"
+    "\n",
+    ""
    ]
   },
   {

docs/quickstart.rst

@@ -16,7 +16,7 @@ Key features:
 * Support for proteogenomic approaches at the interface of transcriptomics and proteomics.
 * Various data visualizations.
 
-.. image:: notebooks/Isotools_overview_slide.png
+.. image:: notebooks/Isotools_overview.png
   :width: 800
   :alt: IsoTools overview