diff --git a/.gitignore b/.gitignore
index 60c984b..f6b5ff3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -39,3 +39,6 @@ hs_err_pid*
/isopret-interpro-overrep.txt
/isopret-gui_1.0.0-1_amd64.deb
/isopret-gui-1.0.0-M1.dmg
+.vscode/
+isopret-io/target/
+venv/
\ No newline at end of file
diff --git a/README.md b/README.md
index a1dc5e4..a59d93a 100644
--- a/README.md
+++ b/README.md
@@ -60,6 +60,7 @@ Enter the following code to install mkdocs and run a server locally. The GitHub
```
python3 -m venv venv
source venv/bin/activate
+pip install mkdocs
pip install mkdocs-material
pip install mkdocs-material[imaging]
pip install mkdocs-material-extensions
diff --git a/docs/index.md b/docs/index.md
index a06c657..459ce01 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -12,10 +12,6 @@ Isopret uses the analysis (output) file of
TODO -- point to tutorial amd also mention EDGER
-HBA-DEALS
-analyzes RNA-Seq data to determine differentially expression and differential
-splicing simultaneous. Isopret then performs
-Gene Ontology analysis using a Java 17 implementation of code from
-the [Ontologizer](https://pubmed.ncbi.nlm.nih.gov/18511468/){:target="_blank"}.
+HBA-DEALS analyzes RNA-Seq data to determine differentially expression and differential splicing simultaneous. Isopret then performs Gene Ontology analysis using an updated implementation of code from the [Ontologizer](https://pubmed.ncbi.nlm.nih.gov/18511468/){:target="_blank"}.
diff --git a/docs/input.md b/docs/input.md
index eee1ce0..880dd22 100644
--- a/docs/input.md
+++ b/docs/input.md
@@ -11,11 +11,15 @@ Hierarchical Bayesian Analysis of Differential Expression and ALternative Splici
simultaneously characterizes differential expression and splicing in cohorts.
-.. figure:: /img/hbadeals.png
- :width: 80%
- :align: center
- HBA-DEALS. The log-transformed expression of a gene with three isoforms (green, orange, and blue) is shown. The gene expression is the sum of the expression of the isoforms. Differential gene expression is modeled as two Normal distributions whose means differ by the parameter β. The proportions of the corresponding isoforms have a Dirichlet prior, and the difference in proportions between controls and cases is modeled by α (symbolized by the two triangles). An MCMC procedure is used to solve for the posterior distribution of the parameters of the model for all genes and isoforms at once.
+
+{ width="1000" }
+HBA-DEALS..
+
+
+
+
+The log-transformed expression of a gene with three isoforms (green, orange, and blue) is shown. The gene expression is the sum of the expression of the isoforms. Differential gene expression is modeled as two Normal distributions whose means differ by the parameter β. The proportions of the corresponding isoforms have a Dirichlet prior, and the difference in proportions between controls and cases is modeled by α (symbolized by the two triangles). An MCMC procedure is used to solve for the posterior distribution of the parameters of the model for all genes and isoforms at once.
The HBA-DEALS algorithm is explained in [Karlebach et al, 2020, Genome Biology 21:171](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6).
Source code is available at the [HBA-DEALS GitHub repository](https://github.com/TheJacksonLaboratory/HBA-DEALS).
@@ -64,7 +68,7 @@ only [Ensembl](http://ensembl.org/) gene/transcript models.
## Running HBA-DEALS
-A Snakemake pipeline for running HBA-DEALS is described in the
+A Snakemake pipeline for running HBA-DEALS is described in the
[GitHub repository](https://github.com/TheJacksonLaboratory/covid19splicing)
for the paper [Betacoronavirus-specific alternate splicing](https://pubmed.ncbi.nlm.nih.gov/35074468/). The GitHub repository
also contains 15 HBA-DEALS output files related to that publication that can be used as input for Isopret-Gui.
diff --git a/docs/output.md b/docs/output.md
index f521fbe..24166b1 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -15,7 +15,7 @@ false discovery rate (FDR) are highlighted in color.
-{ width="1000" }
+{ width="1000" }
IsopretGO overview tab.
@@ -33,7 +33,7 @@ and analysis results for that gene. The tab has three parts -- isoforms, protein
The isoform section shows the structure of each isoform that has at least one read in the RNA-seq data.
-{ width="1000" }
+{ width="1000" }
IsopretGO gene tab, isoforms section.
@@ -57,7 +57,7 @@ at the top of the table and highlighted green.
-{ width="1000" }
+{ width="1000" }
IsopretGO gene tab, Gene Ontology section.
@@ -83,20 +83,24 @@ Clicking on the ``Compare DGE & DAS`` button will open a dialog that shows the n
of GO terms to compare results for expression and splicing.
-{ width="1000" }
+{ width="1000" }
IsopretGO gene tab, Gene Ontology DAS tab.
-.. figure:: /img/isopret8.png
- :width: 70%
- :align: center
- Isopret. Gene Ontology tab, compare differential expression and differential splicing
+
+
+{ width="1000" }
+Gene Ontology tab, compare differential expression and differential splicing
+
+
+
+
+
-Clicking on the ``Export`` button next to a GO term will show summaries for each gene that is annotated to the GO term
+Clicking on the **Export** button next to a GO term will show summaries for each gene that is annotated to the GO term
and is also differentially expressed (for DGE) or spliced (for DAS). This generates an HTML page that can be
-used to explore the genes associated with the GO term together with their corresponding patterns of differential expression and splicing
-Note that the output is restricted to the first 100 genes to limit the size of the resulting HTML page.
+used to explore the genes associated with the GO term together with their corresponding patterns of differential expression and splicing. Note that the output is restricted to the first 100 genes to limit the size of the resulting HTML page.
diff --git a/docs/running-gui.md b/docs/running-gui.md
index 36f522c..64431ff 100644
--- a/docs/running-gui.md
+++ b/docs/running-gui.md
@@ -18,7 +18,7 @@ java -jar Isopret.jar
-{ width="1000" }
+{ width="1000" }
Appearance of the app when started for the first time.
@@ -48,7 +48,7 @@ The drawback of the term-for-term approach is that it does not respect dependenc
are caused by overlapping annotations. As a result of the true-path rule, each term in GO shares all the
annotations of all of its descendants. Isopret also offers two algorithms for GO analysis that
assess GO term overrepresentation that examines each term in the context of its parent terms,
-which we call the parent–child approach
+which we call the parent–child approach
([Grossmann et al., 2007](https://academic.oup.com/bioinformatics/article/23/22/3024/208216?login=false)).
In our experiments, the ``parent–child-intersection`` approach is generally more conservative than
the ``parent–child-union`` approach.
@@ -57,13 +57,13 @@ the ``parent–child-union`` approach.
Isopret offers the following multiple-testing correction options for the GO analysis: Bonferroni, Bonferroni-Holm,
-Sidak, Benjamini-Hochberg, Benjamini-Yukutieli, None. The book
+Sidak, Benjamini-Hochberg, Benjamini-Yukutieli, None. The book
[Introduction to Bio-Ontologies](https://www.routledge.com/Introduction-to-Bio-Ontologies/Robinson-Bauer/p/book/9780367659271)
provides detailed explanations of the GO Overrepresentation analysis procedures and multiple testing correction approaches.
{ width="1000" }
-Appearance of the app after data download with an HBA-DEAL file chosen and the analysis set to
+Appearance of the app after data download with an HBA-DEAL file chosen and the analysis set to
Parent-Child Intersection with Benjamini-Hochberg MTC.
diff --git a/docs/running-inferrence.md b/docs/running-inferrence.md
index 54db771..a9de362 100644
--- a/docs/running-inferrence.md
+++ b/docs/running-inferrence.md
@@ -1,14 +1,16 @@
-.. _rstrunninginferrence:
+# Inference
+
+
-=====================================
-Running the isopret inferrence script
-=====================================
Here, we explain how to set up and run the R scripts developed to perform expectation-maximization analysis to infer
GO annotations for isoforms.
+## Running the isopret inferrence script
+
+
The scripts are stored in the directory ``em-scripts`` in the project
-`GitHub repository `_.
+[GitHub repository](https://github.com/TheJacksonLaboratory/isopret).
The script ``translate_all_isoforms.R`` can be used for obtaining isoform amino-acid sequences. It extracts isoform coordinates from a .gtf file and calls the tool gffread to translate the genomic sequence. The variables containing the paths to the .fasta file containing the genome sequence and the .gtf file with isoform coordinates ('fasta.file' and 'gtf.file', respectively) should match the locations of the files in the system.
diff --git a/docs/setup.md b/docs/setup.md
index 0c31734..fda5631 100644
--- a/docs/setup.md
+++ b/docs/setup.md
@@ -22,21 +22,24 @@ build isopret-gui from source, then the build process described below requires
Go the GitHub page of [isopretGO](https://github.com/TheJacksonLaboratory/isopretGO), and clone the project.
-Build the executable from source with maven, and then test the build. ::
-
- git clone https://github.com/TheJacksonLaboratory/isopret.git
- cd isopret
- mvn package
- java -jar target/isopret.jar
- Usage: isopret [-hV] [COMMAND]
- Isoform interpretation tool.
- -h, --help Show this help message and exit.
- -V, --version Print version information and exit.
- Commands:
- download, D Download files for prositometry
- hbadeals, H Analyze HBA-DEALS files
- svg, V Create SVG/PDF files for a specific gene
- stats, S Show descriptive statistics about data
+Build the executable from source with maven, and then test the build.
+
+```bash
+git clone https://github.com/TheJacksonLaboratory/isopret.git
+cd isopret
+mvn package
+java -jar target/isopret.jar
+ Usage: isopret [-hV] [COMMAND]
+ Isoform interpretation tool.
+ -h, --help Show this help message and exit.
+ -V, --version Print version information and exit.
+ Commands:
+ download, D Download files for prositometry
+ hbadeals, H Analyze HBA-DEALS files
+ svg, V Create SVG/PDF files for a specific gene
+ stats, S Show descriptive statistics about data
+```
+