Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Gene set variation analysis

pathfindR: Enrichment Analysis Utilizing Active Subnetworks

CAusal Reasoning for Network Identification with integer VALue programming in R

Lightweight Iterative Gene set Enrichment in R

Explore the cancer relevance of your gene list

From RNA-seq raw reads to enriched pathways by DEGs

Analysis and visualization of RNA-Seq results

R package for visualising high-dimensional categorical data

Multi-Enrichment Analysis of Gene Set Enrichment Analysis Results

Explore biomolecular pathways in Reactome from the command-line or a Python script

Python Client Package for WikiPathways

TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis

The Kinase Library: a Global Atlas of the Human Protein Kinome

A Python package for benchmarking pathway database with functional enrichment and classification methods

Single sample pathway analysis tools for omics data

WikiPathways Database

A Python package for metabolite enrichment analysis.

FunMappOne: a tool to summarize and visually navigate functional categories in multiple experiments.

R package for de novo pathway enrichment using KeyPathwayMiner

Representation and Quantification Of Module Activity in Single Cells

Cellular​ ​signatures​ characterisation ​after​ ​carcinogenic​ ​chemical​ ​exposure​ ​in​ ​mammalian​ ​tissue.

Curated list of analysis pipelines for biological & clinical interpretation of data-driven findings

GWAS of Postmortem Brain Samples Sheds Light on the Development of Schizophrenia and Bipolar Disorder

Pipeline to extract bacterial protein sequences, generate Bacformer embeddings, compute genome-level cosine similarity, cluster related strains, and interpret results using pangenome analysis, pathway enrichment, and RAG-based functional annotation.

WikiPathways Summit Planning

Web application that enables users to compare the expression of genes or enrichment of gene sets between different molecular subtypes of colorectal cancer

An interactive R Shiny web app for DNA methylation analysis with support for DE, pathway enrichment, power analysis, and machine learning — deployable on HPC via Singularity/Apptainer.

Just another wrapper for pathway analysis using MAGMA

Python and R programs used in the identification of repurposed drugs against viruses responsible for causing epidemics/pandemics