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

MSigDB gene sets for multiple organisms in a tidy data format

BioBombe: Sequentially compressed gene expression features enhances biological signatures

Lightweight Iterative Gene set Enrichment in R

Evolutionary Transcriptomics with R

📊 Identify cell types and pathways affected by genetic risk loci.

Package to calculate functional similarity between genes https://biocor.llrs.dev

Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)

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

A web application for exploring, analyzing, and curating pathway databases

A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)

An r interface to perform ROMA

resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

💹 The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center …

Full results to accompany Zhu and Stephens (2018).

R wrapper for ermineJ

COVID-19 Crowd Generated Gene and Drug Set Library

gene-set clustering and network visualization

Package to analyse gene sets

Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data