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DiffBind

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: Release (3.17)

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")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DiffBind")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

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

Details

biocViews ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software
Version 3.10.0
In Bioconductor since BioC 2.9 (R-2.14) (12 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
Linking To Rhtslib(>= 1.99.1), Rcpp
Suggests BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid
System Requirements GNU make
Enhances
URL https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/DiffBind
See More
Depends On Me ChIPQC, vulcan
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DiffBind_3.10.0.tar.gz
Windows Binary DiffBind_3.10.0.zip (64-bit only)
macOS Binary (x86_64) DiffBind_3.10.0.tgz
macOS Binary (arm64) DiffBind_3.10.0.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/
Package Downloads Report Download Stats