1. Welcome to GSEAPY’s documentation!

1.1. GSEAPY: Gene Set Enrichment Analysis in Python.

1.2. GSEApy is a Python/Rust implementation of GSEA and wrapper for Enrichr.

It’s used for convenient GO enrichments and produce publication-quality figures from python.

GSEApy could be used for RNA-seq, ChIP-seq, Microarry data.

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

The full GSEA is far too extensive to describe here; see GSEA documentation for more information.

Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr .

1.3. 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

1.4. Installation

Install gseapy package from bioconda or pypi.

# if you have conda (MacOS_x86-64 and Linux only)
$ conda install -c bioconda gseapy

# or use pip to install the latest release
$ pip install gseapy

1.5. GSEA Java version output:

This is an example of GSEA desktop application output

1.6. GSEApy `Prerank` module output

Using the same data from GSEA, GSEApy reproduces the example above.

Using Prerank or replot module will reproduce the same figure for GSEA Java desktop outputs

_images/gseapy_OCT4_KD.png — Generated by GSEAPY

**GSEApy figures are supported by all matplotlib figure formats.**

You can modify `GSEA` plots easily in .pdf files. Please Enjoy.

1.7. GSEApy `enrichr` module

A graphical introduction of Enrichr

The only thing you need to prepare is a gene list file in txt format(one gene id per row), or a python list object.

Note: Enrichr uses a list of Entrez gene symbols as input. You should convert all gene names to uppercase.

For example, both a list object and txt file are supported for enrichr API

# if you prefer to run gseapy.enrchr() inside python console, you could assign a list object to
# gseapy like this.
gene_list = ['SCARA3', 'LOC100044683', 'CMBL', 'CLIC6', 'IL13RA1', 'TACSTD2', 'DKKL1',
                'CSF1', 'CITED1', 'SYNPO2L']

# an alternative way is that you could provide a gene list txt file which looks like this:
with open('data/gene_list.txt') as genes:
    print(genes.read())


CTLA2B
SCARA3
LOC100044683
CMBL
CLIC6
IL13RA1
TACSTD2
DKKL1
CSF1
CITED1
SYNPO2L
TINAGL1
PTX3

1.8. Installation