Merge pull request #173 from TheJacksonLaboratory/develop

Develop

.github/workflows/documentation.yaml

@@ -2,7 +2,7 @@ name: mkdocs-generation
 on:
   push:
     branches:
-      - master
+      - develop
       - main
 permissions:
   contents: write

README.md

@@ -2,19 +2,24 @@
 
 Isoform Interpretation (isopret) with Gene Ontology (isopretGO) is Java desktop application to 
 visualize the functional implications of differential gene expression and differential alternative splicing
-in RNA-seq data. isopretGO leverages isoform-specific functional (GO) annotations presented in
-[Karlebach G, et al. (2023) Bioinformatics 39:btad132](https://pubmed.ncbi.nlm.nih.gov/36929917/)
-for an approach towards GO overrepresentation analysis of differential transcripts, and presents
-a graphicual user interface (GUI) application to perform the analysis and explore the results.
+in RNA-seq data. 
+
+
+|            Setup            | Overview | Gene visualization |
+|:---------------------------:|:-------------------------:|:-------------------------:|
+|  ![](docs/img/isopret1.png) | ![](docs/img/isopret3.png) | ![](docs/img/isopret4.png) |
+
+|    Protein visualization    | Inferred isoform specific GO | GO overrepresentation |
+|:---------------------------:|:----------------------------:|:-------------------------:|
+|  ![](docs/img/isopret5.png) |  ![](docs/img/isopret6.png)  | ![](docs/img/isopret7.png) |
+
+
 
 See the [online documentation](https://thejacksonlaboratory.github.io/isopretGO/) for installation and usage instructions.
 
+See the [Release page](https://github.com/TheJacksonLaboratory/isopretGO/releases) for the executable JAR file.
 
-interpret the potential biological  functions that are affected by differential alternative splicing. Isopret is
-available as a Java desktop application. Most users should download the latest version from the
-Releases page.
 
-A manuscript is in preparation.
 
 
 

docs/tutorial.md

@@ -0,0 +1,47 @@
+# Tutorial
+
+This tutorial demonstrates how to generate the output shown in parts of the manuscript.
+
+### Setup the graphical user interface (GUI) version of isopretGO
+
+Follow the [instructions](running-gui.md) to download and start isopretGUI. Use the *Download* button (1) to download
+the required input files.
+
+Two HBA-DEALS files are provided for this tutorial in the `tutorial_files` diredtorz of the GitHub repository:
+
+- [Hooks_HBADEALS_output.txt](../tutorial_files/Hooks_HBADEALS_output.txt)
+- [Wagner_HBADEALS_output.txt](../tutorial_files/Wagner_HBADEALS_output.txt)
+
+
+Both files contain the results of analysis of hepatoblastoma datasets. 
+[Hooks KB, et al. (2018) New insights into diagnosis and therapeutic options for proliferative hepatoblastoma. Hepatology. 68:89-102](https://pubmed.ncbi.nlm.nih.gov/29152775/)
+present RNA sequencing of 25 hepatoblastomas and matched normal liver samples. 
+[Wagner AE, et al. (2020) SP8 Promotes an Aggressive Phenotype in Hepatoblastoma via FGF8 Activation. Cancers (Basel) 12:2294](https://pubmed.ncbi.nlm.nih.gov/32824198/)
+present RNA-sequencing of four primary hepatoblastomas with metastasis and seven primary hepatoblastomas without metastasis, 11 matching normal liver specimens and four liver tumor cell lines.
+
+
+### HBA-DEALS input file
+
+Select the file (2) and press the Analyse! button (3).
+
+<figure markdown>
+![Overview tab](./img/isopretSetup.png){ width="800" }
+<figcaption>IsopretGO overview tab.
+</figcaption>
+</figure>
+
+Leave the Gene Ontology (GO) settings in their default values. If desired, other GO overrepresentation algorithms or multiple-testing correction (MTC) procedures can be used. See [Bauer et al. (2008)](https://pubmed.ncbi.nlm.nih.gov/18511468/){:target="\_blank"}. for information and
+[Introduction to Bio-Ontologies](https://www.amazon.de/-/en/Charite-Universitatsmedizin-Berlin-Germany-Robinson/dp/1439836655){:target="\_blank"}. for detailed explanations.
+
+
+### Analysis summary
+After you press the *Analyse!* button, isopretGO will perform the analysis, which should take between 15-60 seconds on typical laptops. A progress bar is shown. isopretGO will then open the **Analysis* tab, which shows a table with all genes measured in the RNA-seq experiment, ordered by posterior error probability (PEP; See [Käll et al. 2008](https://pubmed.ncbi.nlm.nih.gov/18052118/){:target="\_blank"} for a primer on PEP).
+
+<figure markdown>
+![Overview tab](./img/analysis_summary.png){ width="800" }
+<figcaption>IsopretGO Analysis tab.
+</figcaption>
+</figure>
+
+To search for a specific gene, enter the gene symbol in the search bar on the left right underneath the table in this view.
+For instance, enter the symbol MICU1, which refers to the [Mitochondrial Calcium Uptake 1](https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1530){:target="\_blank"} gene.

mkdocs.yml

@@ -44,7 +44,6 @@ nav:
 
 
 plugins:
-  - social
   - search
   - mkdocstrings:
       handlers:
@@ -53,14 +52,6 @@ plugins:
             docstring_style: sphinx
 
 
-extra:
-  social:
-    - icon: fontawesome/brands/github-alt
-      link: https://github.com/pnrobinson
-    - icon: fontawesome/brands/linkedin
-      link: https://www.linkedin.com/in/peter-n-robinson-b7833811/
-
-
 markdown_extensions:
   - pymdownx.highlight:
       anchor_linenums: true
@@ -76,10 +67,7 @@ markdown_extensions:
   - attr_list
   - md_in_html
   - tables
-  - pymdownx.emoji:
-      emoji_index: !!python/name:material.extensions.emoji.twemoji
-      emoji_generator: !!python/name:material.extensions.emoji.to_svg
 
 copyright: |
-  &copy; 2023 <a href="https://github.com/pnrobinson"  target="_blank" rel="noopener">Peter N Robinson</a>
+  &copy; 2024 <a href="https://github.com/pnrobinson"  target="_blank" rel="noopener">Peter N Robinson</a>