Journal article

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

Aaron TL Lun, Gordon K Smyth

NUCLEIC ACIDS RESEARCH | OXFORD UNIV PRESS | Published : 2016

Abstract

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..

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University of Melbourne Researchers

Grants

Awarded by National Health and Medical Research Council Program Grant


Awarded by National Health and Medical Research Council Fellowship


Funding Acknowledgements

The University of Melbourne (Elizabeth and Vernon Puzey scholarship) (to A.T.L.L.); National Health and Medical Research Council Program Grant [1054618 to G.K.S.]; National Health and Medical Research Council Fellowship [1058892 to G.K.S.]; Victorian State Government Operational Infrastructure Support; Australian Government NHMRC IRIIS. Funding for open access charge: National Health and Medical Research Council Program Grant [1054618].