DiffBind

DOI: 10.18129/B9.bioc.DiffBind    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: 3.12

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 "4.0") and enter:

if (!requireNamespace("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, ChIPSeq, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, Sequencing, Software
Version	3.0.15
In Bioconductor since	BioC 2.9 (R-2.14) (9.5 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
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_3.0.15.tar.gz
Windows Binary	DiffBind_3.0.15.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	DiffBind_3.0.15.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