Hongkai’s Research Group
Software & Database
(1) BIRD: genome-wide prediction of chromatin accessibility using RNA-seq or exon array data
(2) CisGenome: integrated software for ChIP-seq and ChIP-chip peak calling, annotation, motif analysis, etc.
(3) ChIP-PED: an R package with graphical user interface for discovering regulatory pathway activities in a large compendium of gene expression data from GEO.
(4) ChIPXpress: improve target gene ranking using gene expression information in Gene Expression Omnibus (GEO).
(5) CorMotif: an R/bioconductor package for jointly analyzing multiple gene expression datasets to simultaneously detect differentially expression genes and patterns.
(6) 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.
(7) 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.
(8) iASeq: an R/bioconductor package for detecting allele-specific binding by jointly analyzing multiple ChIP-seq data sets
(9) JAMIE: joint analysis of multiple ChIP-chip datasets for improving peak calling.
(10) PolyaPeak: a tool for improving ChIP-seq peak calling using peak shape information.
(11) PowerExpress: a tool for finding genes with a user-specified pattern of interest from multiple gene expression experiments.
(12) SCATE: single-cell ATAC-seq signal extraction and enhancement
(13) SCRAT: a toolbox for analyzing single-cell regulome (scATAC-seq, scDNase-seq, scChIP-seq) data.
(14) TileMap: a software tool for ChIP-chip peak calling.
(15) TileProbe: a software tool for removing probe effects in Affymetrix tiling array data.
(16) TSCAN: pseudo-time analysis of single-cell RNA-seq data.