chipseq
chipseq: A package for analyzing chipseq data
Bioconductor version: Release (3.20)
Tools for helping process short read data for chipseq experiments.
Author: Deepayan Sarkar [aut], Robert Gentleman [aut], Michael Lawrence [aut], Zizhen Yao [aut], Oluwabukola Bamigbade [ctb] (Converted vignette from Sweave to R Markdown / HTML.), Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("chipseq")):
Installation
To install this package, start R (version "4.4") 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")| Some Basic Analysis of ChIP-Seq Data | HTML | R Script |
| Reference Manual |
Details
| biocViews | ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software |
| Version | 1.56.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (15 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), 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, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | ChIPQC, soGGi, transcriptR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | chipseq_1.56.0.tar.gz |
| Windows Binary (x86_64) | chipseq_1.56.0.zip |
| macOS Binary (x86_64) | chipseq_1.56.0.tgz |
| macOS Binary (arm64) | chipseq_1.55.0.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 |