CisGenome new software for Chip-Seq

CisGenome - just published in Nov. Nature Biotechnology.

An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH.
Nat Biotechnol. 2008 Nov;26(11):1293-300.

A full-function integrated bioinformatics suite for ChIP-chip and ChIP-Seq including peak-finding, FDR control for single samples, subtraction of control lane, visualization and annotation of peaks on known genomes, and Motif finding.  Functional GUI on Windows and Mac. Wow. 

Software website here:  CisGenome

http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

Abstract:

We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome
is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false
discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously
published ChIP–microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically
for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of
CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode
computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure,
conservation, and DNA sequence and motif information. We demonstrate the use of these tools by a comparative analysis of
ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis with or without a negative
control sample, and an analysis of a new motif in Nanog- and Sox2-binding regions.