- hmChIP: a database of publicly available human and mouse ChIP-seq and ChIP-chip data.
- PDDB: a database of predicted regulatory element activities based on BIRD
- BIRD: genome-wide prediction of chromatin accessibility using RNA-seq or exon array data
- CisGenome: integrated software for ChIP-seq and ChIP-chip peak calling, annotation, motif analysis, etc.
- ChIP-PED: an R package with graphical user interface for discovering regulatory pathway activities in a large compendium of gene expression data from GEO.
- ChIPXpress: improve target gene ranking using gene expression information in Gene Expression Omnibus (GEO).
- CorMotif: an R/Bioconductor package for jointly analyzing multiple gene expression datasets to simultaneously detect differentially expression genes and patterns.
- dPCA: a software tool for analyzing differential binding. It compares the quantitative ChIP-seq signals in multiple ChIP-seq datasets between two biological conditions and considers the variability in replicate samples.
- GSCA: a software tool with graphical user interface for mining publicly available gene expression data. It allows one to systematically identify biological contexts associated with user-specified gene set activity patterns.
- iASeq: an R/Bioconductor package for detecting allele-specific binding by jointly analyzing multiple ChIP-seq data sets
- JAMIE: joint analysis of multiple ChIP-chip datasets for improving peak calling.
- PolyaPeak: a tool for improving ChIP-seq peak calling using peak shape information.
- PowerExpress: a tool for finding genes with a user-specified pattern of interest from multiple gene expression experiments.
- SCATE: an R/Bioconductor package for single-cell ATAC-seq signal extraction and enhancement
- SCRAT: a toolbox for analyzing single-cell regulome (scATAC-seq, scDNase-seq, scChIP-seq) data.
- TileMap: a software tool for ChIP-chip peak calling.
- TileProbe: a software tool for removing probe effects in Affymetrix tiling array data.
- TSCAN: pseudo-time analysis of single-cell RNA-seq data.