To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DiffBind")

In most cases, you don't need to download the package archive at all.

DiffBind

DOI: 10.18129/B9.bioc.DiffBind

Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: Release (3.5)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DiffBind")

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 2.4.8
In Bioconductor since BioC 2.9 (R-2.14) (6 years)
License Artistic-2.0
Depends R (>= 3.3.0), GenomicRanges, SummarizedExperiment
Imports RColorBrewer, amap, edgeR, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, zlibbioc, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools, DESeq2, methods, graphics, ggrepel
LinkingTo Rsamtools(>= 1.19.38), Rcpp
Suggests DESeq, BiocStyle, testthat
SystemRequirements
Enhances rgl, XLConnect
URL
Depends On Me ChIPQC
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package DiffBind_2.4.8.tar.gz
Windows Binary DiffBind_2.4.8.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DiffBind_2.4.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/DiffBind
Package Short Url http://bioconductor.org/packages/DiffBind/
Package Downloads Report Download Stats

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