DiffBind

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see DiffBind.

Differential Binding Analysis of ChIP-Seq Peak Data


Bioconductor version: 3.7

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 "3.5") 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")
DiffBind: Differential binding analysis of ChIP-Seq peak data PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version 2.8.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License Artistic-2.0
Depends R (>= 3.5), 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
System Requirements
URL
See More
Suggests DESeq, BiocStyle, testthat
Linking To Rsamtools(>= 1.19.38), Rcpp
Enhances rgl, XLConnect
Depends On Me ChIPQC, vulcan
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DiffBind_2.8.0.tar.gz
Windows Binary DiffBind_2.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DiffBind_2.8.0.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
Old Source Packages for BioC 3.7 Source Archive