Merge pull request #176 from TheJacksonLaboratory/develop

Develop
TheJacksonLaboratory · Jan 22, 2024 · db0bc80 · db0bc80
2 parents 1a686d2 + d514d45
commit db0bc80
Show file tree

Hide file tree

Showing 12 changed files with 17 additions and 39 deletions.
diff --git a/docs/input.md b/docs/input.md
@@ -76,5 +76,7 @@ also contains 15 HBA-DEALS output files related to that publication that can be
 
 # edgeR
 
+Alternatively [edgeR](https://pubmed.ncbi.nlm.nih.gov/19910308/) can be used to call differential expresison and alternative splicing. We provide an R script to perform the analysis
+and format the results in HBA-DEALS format (which is required to use isopret-GO):
 
-todo
+[edgeR_output.R](../scripts/edgeR_output.R)
diff --git a/docs/running-cmd.md b/docs/running-cmd.md
@@ -5,7 +5,7 @@ Isopret offers most functionality via its graphical user interface (GUI) version
 but does have a command-line tool that can be used to perform Gene Ontology (GO)
 overrepresentation analysis from the shell.
 
-The build process described in :ref:`rstsetup_` creates both a GUI app (in the
+The build process described in [setup](setup.md) creates both a GUI app (in the
 ``isopret-gui/target`` subdirectory) and a command-line app (in
 the ``isopret-cli/target`` subdirectory). It is fine to leave both apps in these
 directories if you like. For the following explanation, we will assume that

diff --git a/docs/running-inferrence.md b/docs/running-inferrence.md
diff --git a/docs/running.md b/docs/running.md
@@ -1,15 +1,11 @@
 # Running isopretGO
 
 
-Isopret offers a  command-line tools that performs Gene Ontology overrepresentation
-analysis with the inferred isoform GO annotations. A GUI version with additional
-visualization tools is in preparation.
-
-- [running-inferrence](running-inferrence.md)
-- [running-cmd](running-cmd.md)
-
-
-
+Isopret-GO offers tools that performs Gene Ontology overrepresentation
+analysis with the inferred isoform GO annotations. 
 
+- [GUI version](running-gui.md)
+- [Command-line version](running-cmd.md)
+- [Exporting PDF files](running-pdf.md)
 
 
diff --git a/docs/setup.md b/docs/setup.md
@@ -63,7 +63,7 @@ pip install mkdocstrings[python]
 mkdocs serve
 ```
 
-Note that on an M! Mac we have encountered a difficulty with mkdocs not finding the cairo library. This can be solved
+Note that on an M1   Mac we have encountered a difficulty with mkdocs not finding the cairo library. This can be solved
 by running
 
 ```

diff --git a/isopret-cli/pom.xml b/isopret-cli/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.1</version>
+        <version>1.3.0</version>
     </parent>
 
     <artifactId>isopret-cli</artifactId>

diff --git a/isopret-core/pom.xml b/isopret-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.1</version>
+        <version>1.3.0</version>
     </parent>
 
     <artifactId>isopret-core</artifactId>

diff --git a/isopret-data/pom.xml b/isopret-data/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.1</version>
+        <version>1.3.0</version>
     </parent>
 
     <artifactId>isopret-data</artifactId>

diff --git a/isopret-exception/pom.xml b/isopret-exception/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.1</version>
+        <version>1.3.0</version>
     </parent>
 
     <artifactId>isopret-exception</artifactId>

diff --git a/isopret-gui/pom.xml b/isopret-gui/pom.xml
@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.1</version>
+        <version>1.3.0</version>
     </parent>
 
     <artifactId>isopret-gui</artifactId>

diff --git a/isopret-io/pom.xml b/isopret-io/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.1</version>
+        <version>1.3.0</version>
     </parent>
     <packaging>jar</packaging>
     <artifactId>isopret-io</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
     </parent>
     <groupId>org.jax.isopret</groupId>
     <artifactId>isopret</artifactId>
-    <version>1.2.1</version>
+    <version>1.3.0</version>
     <modules>
         <module>isopret-core</module>
         <module>isopret-cli</module>