DOI: 10.18129/B9.bioc.DiffBind  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: 3.16

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Author: Rory Stark [aut, cre], Gord Brown [aut]

Maintainer: Rory Stark <rory.stark at cruk.cam.ac.uk>

Citation (from within R, enter citation("DiffBind")):


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PDF R Script DiffBind: Differential binding analysis of ChIP-Seq peak data
PDF   Reference Manual
Text   NEWS


biocViews ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software
Version 3.8.4
In Bioconductor since BioC 2.9 (R-2.14) (11.5 years)
License Artistic-2.0
Depends R (>= 4.0), GenomicRanges, SummarizedExperiment
Imports RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools(>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP
LinkingTo Rhtslib(>= 1.99.1), Rcpp
Suggests BiocStyle, testthat, xtable
SystemRequirements GNU make
Enhances rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid
URL https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/DiffBind
Depends On Me ChIPQC, vulcan
Imports Me
Suggests Me
Links To Me
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Source Package DiffBind_3.8.4.tar.gz
Windows Binary DiffBind_3.8.4.zip (64-bit only)
macOS Binary (x86_64) DiffBind_3.8.4.tgz
macOS Binary (arm64) DiffBind_3.8.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/DiffBind
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DiffBind
Bioc Package Browser https://code.bioconductor.org/browse/DiffBind/
Package Short Url https://bioconductor.org/packages/DiffBind/
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