Cistrome 
Constructing

Model-based Analysis of ChIP-Seq (MACS) 
A model-based algorithm for finding enriched regions in ChIP-Seq experiments.

Generalized fold change (GFOLD) 
Generalized fold change for ranking differentially expressed genes from RNA-seq data.

Binding and Expression Target Analysis (BETA) 
Targets analysis pipeline by integration of transcriptome and ChIP-seq data.

ChiLin 

ChiLin is an extensible software suite that is ideal for processing and quality control of large batches of ChIP-seq and DNase-seq data.

Publication submitted.