chipseq
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see chipseq.
chipseq: A package for analyzing chipseq data
Bioconductor version: 3.9
Tools for helping process short read data for chipseq experiments
Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R, enter
citation("chipseq")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chipseq")
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("chipseq")| A Sample ChIP-Seq analysis workflow | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software |
| Version | 1.34.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (14.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), methods, BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), ShortRead |
| Imports | methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene |
| Linking To | |
| Enhances | |
| Depends On Me | PING |
| Imports Me | ChIPQC, CopywriteR, HTSeqGenie, soGGi, transcriptR |
| Suggests Me | GenoGAM, ggbio |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | chipseq_1.34.0.tar.gz |
| Windows Binary | chipseq_1.34.0.zip |
| Mac OS X 10.11 (El Capitan) | chipseq_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/chipseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/chipseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/chipseq/ |
| Package Short Url | https://bioconductor.org/packages/chipseq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |