pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Lightweight Iterative Gene set Enrichment in R

Enrichment Networks for Pathway Enrichment Analysis

Chemical Similarity Enrichment analysis of metabolomics datasets

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

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

Read HOMER motif analysis output in R.

mulea - an R package for enrichment analysis using various ontologies and empirical FDR correction

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing

🎣 Bioconductor package for pathway enrichment and depletion analysis via a Fisher's exact test on custom test sets and annotations

Function Enrichment analysis and Network construction

R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.

Ready-to-use curated genesets for cinaR

The goal of LRcell is to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. To achieve this, LRcell utilizes sets of cell marker genes acquired from single-cell RNA-sequencing (scRNA-seq) as indicators for various cell types in the tissue of interest. Next, for each cell t…

Population-based pathway analysis of SNP-SNP coevolution

# PeerJ Special Issue on Seagrass for International Association for Biological Oceanography | September 2023 Seagrass nitrogen enrichment experiment, Laamu Maldives, January 2022. SANH project. Collaboration with University of Edinburgh and Maldives Resilient Reefs.

R Package for preprocessing, normalizing, and analyzing proteomics data

A shiny app to perform pathway, drug, brain cell type and brain region (based on the Allen Brain Atlas data) enrichment and visualize the results.