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TheJacksonLaboratory · Jan 22, 2024 · d514d45 · d514d45
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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
 
 ```