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("DiffBind")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, DifferentialPeakCalling, Sequencing, Software |
| Version | 2.12.0 |
| 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, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools(>= 1.99.1), DESeq2, methods, graphics, ggrepel |
| System Requirements | |
| URL |
See More
| Suggests | DESeq, BiocStyle, testthat |
| Linking To | Rhtslib(>= 1.15.3), 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_2.12.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/DiffBind/ |
| Package Short Url | https://bioconductor.org/packages/DiffBind/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |