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

BioBombe: Sequentially compressed gene expression features enhances biological signatures

A repository for the Playbook Workflow Builder project.

Evolutionary Transcriptomics with R

MSigDB gene sets for multiple organisms in a tidy data format

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

Lightweight Iterative Gene set Enrichment in R

An r interface to perform ROMA

R wrapper for ermineJ

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.

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

Code and resources related to the olfactory regeneration project

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

An open-source webserver that allows for easy, reproducible genomics analyses between different webservers

DBRetina python package

gene-set clustering and network visualization

A client for an open-source web app that allows creating, sharing, and analyzing gene sets

Experimental version of data package associated with chipenrich

A python package that consists of functions that process publicly available annotated sets of genes

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