DiffBind

DOI: 10.18129/B9.bioc.DiffBind    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: 3.14

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>

Installation

To install this package, start R (version "4.1") 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")

 

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

Details

biocViews	ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software
Version	3.4.11
In Bioconductor since	BioC 2.9 (R-2.14) (10.5 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(>= 2.0), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP
LinkingTo	Rhtslib(>= 1.15.3), 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
Build Report

Package Archives

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

Source Package	DiffBind_3.4.11.tar.gz
Windows Binary	DiffBind_3.4.11.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	DiffBind_3.4.11.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