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biocLite("DiffBind")
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DiffBind
Differential Binding Analysis of ChIP-Seq peak data
Bioconductor version: 3.0
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>, Gordon Brown <gordon.brown at cruk.cam.ac.uk>
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:
source("http://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 | 1.12.3 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15.0), GenomicRanges, limma, GenomicAlignments |
| Imports | RColorBrewer, amap, edgeR(>= 2.3.58), gplots, grDevices, stats, utils, IRanges, zlibbioc, lattice, S4Vectors |
| LinkingTo | Rsamtools |
| Suggests | DESeq, Rsamtools, DESeq2, BiocStyle |
| SystemRequirements | |
| Enhances | rgl, parallel, BiocParallel |
| URL | |
| Depends On Me | ChIPQC, MMDiff |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DiffBind_1.12.3.tar.gz |
| Windows Binary | DiffBind_1.12.3.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DiffBind_1.12.3.tgz |
| Mac OS X 10.9 (Mavericks) | DiffBind_1.12.3.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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