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DiffBind

Provides functions for processing ChIP-seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-seq peak callers and aligned sequence read datasets. DiffBind is designed to work with multiple peak sets simultaneously, representing different ChIP experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. The primary emphasis of the package is on identifying sites that are differentially bound between two sample groups. It includes functions to support the processing of peak sets, including overlapping and merging peak sets, counting sequencing reads overlapping intervals in peak sets, and identifying statistically significantly differentially bound sites based on evidence of binding affinity (measured by differences in read densities).

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DiffBind forum

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DiffBind classification

DiffBind specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
1.16.0
Requirements:
GenomicRanges, SummarizedExperiment, limma, GenomicAlignments, locfit

DiffBind distribution

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DiffBind support

Documentation

Maintainer

  • Rory Stark <>

Credits

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Publications

Institution(s)

Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK

Link to literature

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