diff --git a/docs/gseapy_tutorial.rst b/docs/gseapy_tutorial.rst index 4c885a5..1010e95 100644 --- a/docs/gseapy_tutorial.rst +++ b/docs/gseapy_tutorial.rst @@ -30,7 +30,7 @@ One thing you should know is that the gseapy input files are the same as ``GSEA`` desktop required. You can use these files below to run ``GSEA`` desktop, too. -1. Prepare an tabular text file of gene expression like this: +Prepare an tabular text file of gene expression like this: ------------------------------------------------------------------ **RNA-seq,ChIP-seq, Microarry data** are all supported. @@ -121,7 +121,7 @@ Here is to see what the structure of expression table looks like -2. An cls file is also expected. +An cls file is also expected. ----------------------------------------------- This file is used to specify column attributes in step 1, just like ``GSEA`` asked. @@ -160,7 +160,7 @@ So you could prepare the cls file in python like this -3. Gene_sets file in gmt format. +Gene_sets file in gmt format. ----------------------------------------------------- All you need to do is to download gene set database file from ``GSEA`` or ``Enrichr`` website. diff --git a/docs/introduction.rst b/docs/introduction.rst index b943a10..1ed322a 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -24,15 +24,6 @@ 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**. -------------------------------------------------------------------------------------------- @@ -52,6 +43,29 @@ The full ``GSEA`` is far too extensive to describe here; see Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr . +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 + + + +Installation +------------ + +Install gseapy package from bioconda or pypi. + + +.. code:: shell + + # if you have conda + $ conda install -c conda-forge -c bioconda gseapy + + # or use pip to install the latest release + $ pip install gseapy + GSEA Java version output: ------------------------------------------------- @@ -140,24 +154,8 @@ Installation # or use pip to install the latest release $ pip install gseapy -| You may instead want to use the development version from Github, by running - -.. code:: shell - - $ pip install git+git://github.com/BioNinja/gseapy.git#egg=gseapy - -Dependency --------------- -* Python 3.7+ -Mandatory -~~~~~~~~~ -* Numpy -* Scipy -* Pandas -* Matplotlib -* Requests(for enrichr API) For API information to use this library, see the :ref:`run`. \ No newline at end of file