csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.
Aaron T L Lun, Gordon K Smyth
Author Information
Aaron T L Lun: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia.
Gordon K Smyth: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia smyth@wehi.edu.au.
Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify binding sites for a target protein in the genome. An important scientific application is to identify changes in protein binding between different treatment conditions, i.e. to detect differential binding. This can reveal potential mechanisms through which changes in binding may contribute to the treatment effect. The csaw package provides a framework for the de novo detection of differentially bound genomic regions. It uses a window-based strategy to summarize read counts across the genome. It exploits existing statistical software to test for significant differences in each window. Finally, it clusters windows into regions for output and controls the false discovery rate properly over all detected regions. The csaw package can handle arbitrarily complex experimental designs involving biological replicates. It can be applied to both transcription factor and histone mark datasets, and, more generally, to any type of sequencing data measuring genomic coverage. csaw performs favorably against existing methods for de novo DB analyses on both simulated and real data. csaw is implemented as a R software package and is freely available from the open-source Bioconductor project.
References
PLoS One. 2013 Jun 10;8(6):e65598
[PMID: 23762400]
