Enables Gene Ontology (and other feature annotation) enrichment calculations and comparisons between feature sets.
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Updated
May 10, 2024 - R
Enables Gene Ontology (and other feature annotation) enrichment calculations and comparisons between feature sets.
Tools to prepare and analyze a priori molecular signatures, such as gene sets.
Package to calculate functional similarity between genes https://biocor.llrs.dev
Evolutionary Transcriptomics with R
muleaData is an ExperimentHubData Bioconductor package for the mulea R package
💹 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 …
📊 Identify cell types and pathways affected by genetic risk loci.
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
GMT files for the mulea R package
Web application that enables users to compare the expression of genes or enrichment of gene sets between different molecular subtypes of colorectal cancer
Experimental version of data package associated with chipenrich
A web application for exploring, analyzing, and curating pathway databases
Analysis of enrichment of gene sets with a GUI and CLI
DBRetina python package
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)
MSigDB gene sets for multiple organisms in a tidy data format
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.
Reference implementation of the paper Redundancy-aware unsupervised ranking based on game theory - application to gene enrichment analysis
An open-source webserver that allows for easy, reproducible genomics analyses between different webservers
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