DiffBind

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: Development (3.24)

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")):

Rory Stark, Gord Brown. DiffBind: Differential Binding Analysis of ChIP-Seq Peak Data. doi:10.18129/B9.bioc.DiffBind, R package version 3.23.6, https://bioconductor.org/packages/DiffBind.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software
Version	3.23.6
In Bioconductor since	BioC 2.9 (R-2.14) (15 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://bioconductor.org/packages/DiffBind/

Suggests	BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, rtracklayer, grid, EnrichedHeatmap, ComplexHeatmap, circlize
Linking To	Rhtslib (>= 1.99.1), Rcpp
Enhances
Depends On Me	ChIPQC, vulcan
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DiffBind_3.23.6.tar.gz
Windows Binary (x86_64)	DiffBind_3.23.6.zip
macOS Binary (big-sur-x86_64)	DiffBind_3.23.6.tgz
macOS Binary (sonoma-arm64)	DiffBind_3.23.6.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DiffBind
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DiffBind
Package Short Url	https://bioconductor.org/packages/DiffBind/
Package Downloads Report	Download Stats