citation

zqfang · Nov 26, 2022 · 754eabf · 754eabf
1 parent bd02ef3
commit 754eabf
Show file tree

Hide file tree

Showing 4 changed files with 39 additions and 20 deletions.
diff --git a/README.rst b/README.rst
@@ -28,27 +28,19 @@ GSEApy: Gene Set Enrichment Analysis in Python.
 .. image:: https://img.shields.io/pypi/pyversions/gseapy.svg
     :alt: PyPI - Python Version
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3748084.svg
-   :target: https://doi.org/10.5281/zenodo.3748084
-
-
-
 
 **Release notes** : https://github.com/zqfang/GSEApy/releases
 
 `Tutorial for scRNA-seq datasets <https://gseapy.readthedocs.io/en/latest/singlecell_example.html#>`_
 
 `Tutorial for general usage <https://gseapy.readthedocs.io/en/latest/gseapy_example.html>`_
 
-To get help of GSEApy
-------------------------------------
-
-1. See `Frequently Asked Questions <https://gseapy.readthedocs.io/en/latest/faq.html>`_
-
-2. Visit the document site at `Examples <https://gseapy.readthedocs.io/en/latest/gseapy_example.html>`_
 
-3. The GSEApy discussion channel: `Q&A <https://github.com/zqfang/GSEApy/discussions>`_ 
+Citation
+------------------------------------
+::
 
+    Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python, Bioinformatics, 2022;, btac757, https://doi.org/10.1093/bioinformatics/btac757
 
 
 
@@ -101,6 +93,7 @@ Using the same data for ``GSEAPreranked``, and ``GSEApy`` reproduce similar resu
 
 See more output here: `Example <http://gseapy.readthedocs.io/en/master/gseapy_example.html>`_
 
+
 Installation
 ------------
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -29,12 +29,20 @@ GSEAPY: Gene Set Enrichment Analysis in Python.
 .. image:: https://img.shields.io/pypi/pyversions/gseapy.svg
     :alt: PyPI - Python Version
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3748085.svg
-   :target: https://doi.org/10.5281/zenodo.3748085
 
 
 **Release notes** : https://github.com/zqfang/GSEApy/releases 
 
+
+Citation
+------------------------------------
+::
+
+    Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python, Bioinformatics, 2022;, btac757, https://doi.org/10.1093/bioinformatics/btac757
+
+
+
+
 GSEApy is a Python/Rust implementation of **GSEA** and wrapper for **Enrichr**. 
 --------------------------------------------------------------------------------------------
 

diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -24,6 +24,14 @@ GSEAPY: Gene Set Enrichment Analysis in Python.
 
 
 
+Citation
+------------------------------------
+::
+
+    Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python, Bioinformatics, 2022;, btac757, https://doi.org/10.1093/bioinformatics/btac757
+
+
+
 GSEApy is a Python/Rust implementation of **GSEA** and wrapper for **Enrichr**.  
 --------------------------------------------------------------------------------------------
 

diff --git a/docs/run.rst b/docs/run.rst
@@ -9,21 +9,20 @@ Developmental Guide
 Module APIs
 ---------------------
 
-
 .. autofunction:: gsea()
 
-
 .. autofunction:: prerank()
 
 .. autofunction:: ssgsea()
 
-
 .. autofunction:: enrichr()
 
+.. autofunction:: enrich()
+
 .. autofunction:: replot()
 
 
-Interface
+GSEA Statistics
 -------------------------
 .. automodule:: gseapy.gsea
    :members:
@@ -32,6 +31,13 @@ Interface
    :members:
 
 
+Over-representation Statistics
+-------------------------------------------------------
+
+.. automodule:: gseapy.stats
+   :members:
+
+
 Enrichr API
 --------------------------
 
@@ -62,7 +68,11 @@ Visualization
 
 
 Scientific Journal and Sci- themed Color Palettes
---------------------------
+-------------------------------------------------------
 
 .. automodule:: gseapy.scipalette
-   :members:
+   :members:
+
+
+Utils
+-------------------------------------------------------