Hongkai’s Research Group

Software & Database

(1) hmChIP: a database of publicly available human and mouse ChIP-seq and ChIP-chip data.

(1) CisGenome: integrated software for peak calling, annotation, motif analysis, etc.

(2) 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.

(3) iASeq: an R/bioconductor package for detecting allele-specific binding by jointly analyzing multiple ChIP-seq data sets

(4) PolyaPeak: a tool for improving ChIP-seq peak calling using peak shape information.

(5) TileMap: a software tool for ChIP-chip peak calling.

(6) TileProbe: a software tool for removing probe effects in Affymetrix tiling array data.

(7) JAMIE: joint analysis of multiple ChIP-chip datasets for improving peak calling.

(8) ChIPXpress: improve target gene ranking using gene expression information in Gene Expression Omnibus (GEO).

 

 

2. ChIP-seq and ChIP-chip data analysis:

(1) 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.

(2) ChIP-PED: an R package for discovering regulatory pathway activities  in a large compendium of gene expression data from GEO.

(3) CorMotif: an R/bioconductor package for jointly analyzing multiple gene expression datasets to simultaneously detect differentially expression genes and patterns.

(4) PowerExpress: a tool for finding genes with a user-specified pattern of interest from multiple gene expression experiments.

3. Gene expression data analysis:

(1) CisGenome: de novo motif discovery, known motif mapping, motif enrichment analysis based on matched genomic control regions.

4. Sequence motif analysis:

(1) ChIP-PED: increasing the value of ChIP-seq/ChIP-chip experiments by  expanding discoveries to other cell types using large compendiums of publicly available gene expression data in GEO

(2) CorMotif: integrative analysis of multiple gene expression experiments.

(3) dPCA: integrative analysis of quantitative ChIP-seq signals in multiple datasets for detecting binding differences between different biological conditions.

(4) 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.

(5) iASeq: integrative analysis of multiple ChIP-seq datasets to improve inference of allele-specificity.

(6) JAMIE: joint analysis of multiple ChIP-chip datasets for improving peak calling

(7) TileProbe: using publicly available ChIP-chip data in GEO to improve probe effect model in the tiling array data.

 

5. Data integration and data mining:

(1) TSCAN: pseudo-time analysis of single-cell RNA-seq data.

(2) SCRAT: a toolbox for analyzing single-cell regulome data.

 

1. Single-cell genomics: