csawBook
This is the released version of csawBook; for the devel version, see csawBook.
The Book of csaw
Bioconductor version: Release (3.23)
Describes how to use the csaw package to detect differentially bound regions in ChIP-seq data. This provides instructions on how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("csawBook")):Aaron Lun. csawBook: The Book of csaw. doi:10.18129/B9.bioc.csawBook, R package version 1.20.0, https://bioconductor.org/packages/csawBook.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("csawBook")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("csawBook")| Link to book | HTML |
| Reference Manual |
Details
| biocViews | EpigeneticsWorkflow, Software, Workflow |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 |
| Depends | BiocFileCache, ChIPpeakAnno, chipseqDBData, csaw, edgeR, Gviz, org.Mm.eg.db, rebook, rmarkdown, Rsamtools, rtracklayer, TxDb.Mmusculus.UCSC.mm10.knownGene |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/csawBook |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/csawBook |
| Package Short Url | https://bioconductor.org/packages/csawBook/ |
| Package Downloads Report | Download Stats |