DiffBind

DOI: 10.18129/B9.bioc.DiffBind    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: 3.9

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Author: Rory Stark<rory.stark at cruk.cam.ac.uk>, Gord Brown <gdbzork at gmail.com>

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 "3.6") 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 ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version 2.12.0
In Bioconductor since BioC 2.9 (R-2.14) (8 years)
License Artistic-2.0
Depends R (>= 3.5), GenomicRanges, SummarizedExperiment
Imports RColorBrewer, amap, edgeR, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools(>= 1.99.1), DESeq2, methods, graphics, ggrepel
LinkingTo Rhtslib(>= 1.15.3), Rcpp
Suggests DESeq, BiocStyle, testthat
SystemRequirements
Enhances rgl, XLConnect
URL
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_2.12.0.tar.gz
Windows Binary DiffBind_2.12.0.zip
Mac OS X 10.11 (El Capitan) DiffBind_2.12.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: