From 8c6697ed6af93efd9b5cdace37252be58b3e82b7 Mon Sep 17 00:00:00 2001
From: Peter Robinson <peter.robinson@jax.org>
Date: Sun, 21 Jan 2024 07:21:54 +0100
Subject: [PATCH 1/3] deleting redundant file

---
 data/isoform2GO(1).xlsx | Bin 21972 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 data/isoform2GO(1).xlsx

diff --git a/data/isoform2GO(1).xlsx b/data/isoform2GO(1).xlsx
deleted file mode 100644
index f6570de59161536df36b4635e6e823a5c61d8a96..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 58852e9bd1f6c02fc455a7f350b7a28d10f828a2 Mon Sep 17 00:00:00 2001
From: Peter Robinson <peter.robinson@jax.org>
Date: Sun, 21 Jan 2024 07:36:21 +0100
Subject: [PATCH 2/3] tutorial files

---
 .github/workflows/documentation.yaml      |     2 +-
 mkdocs.yml                                |    14 +-
 tutorial_files/Hooks_HBADEALS_output.txt  | 41515 ++++++++++++++++
 tutorial_files/README.md                  |     0
 tutorial_files/Wagner_HBADEALS_output.txt | 52367 ++++++++++++++++++++
 5 files changed, 93884 insertions(+), 14 deletions(-)
 create mode 100644 tutorial_files/Hooks_HBADEALS_output.txt
 create mode 100644 tutorial_files/README.md
 create mode 100644 tutorial_files/Wagner_HBADEALS_output.txt

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/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: !!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>
 
diff --git a/tutorial_files/Hooks_HBADEALS_output.txt b/tutorial_files/Hooks_HBADEALS_output.txt
new file mode 100644
index 00000000..d8827ab1
--- /dev/null
+++ b/tutorial_files/Hooks_HBADEALS_output.txt
@@ -0,0 +1,41515 @@
+Gene	Isoform	ExplogFC/FC	P
+ENSG00000000003	Expression	0.00116738297141614	0.9845025
+ENSG00000000003	ENST00000373020	0.99841055902186	0.97051
+ENSG00000000003	ENST00000496771	1.2881064538084	0.23466
+ENSG00000000003	ENST00000614008	1.00221491203677	0.94091
+ENSG00000000419	Expression	-0.00316280070591433	0.986205
+ENSG00000000419	ENST00000371582	1.07372854627394	0.8573475
+ENSG00000000419	ENST00000371584	1.01547839264589	0.9137
+ENSG00000000419	ENST00000371588	0.987906887299234	0.986055
+ENSG00000000419	ENST00000466152	0.956698998326636	0.9126
+ENSG00000000419	ENST00000682366	1.03945654592478	0.910385
+ENSG00000000419	ENST00000682713	1.00097376038368	0.9226375
+ENSG00000000419	ENST00000682754	1.04199454648448	0.9013975
+ENSG00000000419	ENST00000683010	1.12610576088751	0.73167
+ENSG00000000419	ENST00000683048	1.10564650971815	0.78247
+ENSG00000000419	ENST00000684193	0.976807382107721	0.919955
+ENSG00000000419	ENST00000684628	1.03848002243607	0.9007625
+ENSG00000000457	Expression	-0.0225023517569224	0.95616
+ENSG00000000457	ENST00000367771	1.05601863497524	0.9835975
+ENSG00000000457	ENST00000367772	0.884963975512967	0.91127
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diff --git a/tutorial_files/README.md b/tutorial_files/README.md
new file mode 100644
index 00000000..e69de29b
diff --git a/tutorial_files/Wagner_HBADEALS_output.txt b/tutorial_files/Wagner_HBADEALS_output.txt
new file mode 100644
index 00000000..d3b41035
--- /dev/null
+++ b/tutorial_files/Wagner_HBADEALS_output.txt
@@ -0,0 +1,52367 @@
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From 69ea452ff902075faa9e8ff9976b5949f5aa6301 Mon Sep 17 00:00:00 2001
From: Peter Robinson <peter.robinson@jax.org>
Date: Mon, 22 Jan 2024 08:51:52 +0100
Subject: [PATCH 3/3] updating documentation

---
 README.md                 |  21 ++++++++++-------
 docs/img/isopretSetup.png | Bin 0 -> 180548 bytes
 docs/tutorial.md          |  47 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 60 insertions(+), 8 deletions(-)
 create mode 100644 docs/img/isopretSetup.png
 create mode 100644 docs/tutorial.md

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/docs/img/isopretSetup.png b/docs/img/isopretSetup.png
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diff --git a/docs/tutorial.md b/docs/tutorial.md
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+# 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.