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DiffBind

This is the development version of DiffBind; for the stable release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data


Bioconductor version: Development (3.19)

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 <bioconductor at starkhome.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 3.13.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
System Requirements GNU make
URL https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/DiffBind
See More
Suggests BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid
Linking To Rhtslib(>= 1.99.1), Rcpp
Enhances
Depends On Me ChIPQC, vulcan
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DiffBind_3.13.0.tar.gz
Windows Binary DiffBind_3.13.0.zip
macOS Binary (x86_64) DiffBind_3.13.0.tgz
macOS Binary (arm64)
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