:bar_chart: A universal enrichment tool for interpreting omics data

🧬 gget enables efficient querying of genomic reference databases

Gene Set Enrichment Analysis in Python

Python package to perform enrichment analysis from omics data.

Visualization of Functional Enrichment Result

:mask: Disease Ontology Semantic and Enrichment analysis

:books: Biomedical knowledge mining using GOSemSim and clusterProfiler

MSigDB gene sets for multiple organisms in a tidy data format

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

Enrichment Networks for Pathway Enrichment Analysis

🧬 Gene analysis toolkit based on R

Python implementation of Spatial Analysis of Functional Enrichment (SAFE)

Reactome Pathway Analysis

A standalone interactive application for detecting biological significance on a set of genes

This RNAseq data analysis tutorial is created for educational purpose

A Python package for gene network analysis

A set of Shiny apps to provide interactive enrichment analysis and exploration of results.

Multi-Enrichment Analysis of Gene Set Enrichment Analysis Results

Gene Co-expression Network analysis pipeline

rbioapi: User-Friendly R Interface to Biologic Web Services' API

Gene Set Clustering based on Functional annotation

Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.

Flask app for gene over-representation analysis based on Wikidata.

Ultrafast method to compute single-sample gene set enrichment scores for gene expression or proteomics data

A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF

Microarray Analysis Pipeline in Python

Library for KEGG pathway enrichment analysis

ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.

Source code of the R packge BgeeDB to use data from the Bgee database