diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml index 19fdc43a..7bf96a38 100644 --- a/.github/workflows/documentation.yaml +++ b/.github/workflows/documentation.yaml @@ -2,7 +2,7 @@ name: mkdocs-generation on: push: branches: - - master + - develop - main permissions: contents: write diff --git a/README.md b/README.md index 5fc7e6df..ed5ad51f 100644 --- a/README.md +++ b/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. diff --git a/data/isoform2GO(1).xlsx b/data/isoform2GO(1).xlsx deleted file mode 100644 index f6570de5..00000000 Binary files a/data/isoform2GO(1).xlsx and /dev/null differ diff --git a/docs/img/isopretSetup.png b/docs/img/isopretSetup.png new file mode 100644 index 00000000..9feea1ec Binary files /dev/null and b/docs/img/isopretSetup.png differ diff --git a/docs/tutorial.md b/docs/tutorial.md new file mode 100644 index 00000000..bcae7a7d --- /dev/null +++ b/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). + +
+![Overview tab](./img/isopretSetup.png){ width="800" } +
IsopretGO overview tab. +
+
+ +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). + +
+![Overview tab](./img/analysis_summary.png){ width="800" } +
IsopretGO Analysis tab. +
+
+ +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. diff --git a/mkdocs.yml b/mkdocs.yml index ce542cd4..159419b9 100644 --- a/mkdocs.yml +++ b/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: 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