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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
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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")
| R Script | DiffBind: Differential binding analysis of ChIP-Seq peak data | |
| 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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