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Hongkai’s Research Group |
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Software & Database |
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(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.
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