csaw
This is the development version of csaw; for the stable release version, see csaw.
ChIP-Seq Analysis with Windows
Bioconductor version: Development (3.20)
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Author: Aaron Lun [aut, cre], Gordon Smyth [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
Citation (from within R, enter
citation("csaw")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("csaw")
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("csaw")
Introduction | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software |
Version | 1.39.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (10 years) |
License | GPL-3 |
Depends | R (>= 3.5.0), GenomicRanges, SummarizedExperiment |
Imports | Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils |
System Requirements | C++11, GNU make |
URL |
See More
Suggests | AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager |
Linking To | Rhtslib, zlibbioc, Rcpp |
Enhances | |
Depends On Me | csawBook |
Imports Me | diffHic, epigraHMM, extraChIPs, icetea, NADfinder, vulcan, treediff |
Suggests Me | DiffBind, GRaNIE, chipseqDB |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | csaw_1.39.0.tar.gz |
Windows Binary | csaw_1.39.0.zip |
macOS Binary (x86_64) | csaw_1.39.0.tgz |
macOS Binary (arm64) | csaw_1.39.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/csaw |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/csaw |
Bioc Package Browser | https://code.bioconductor.org/browse/csaw/ |
Package Short Url | https://bioconductor.org/packages/csaw/ |
Package Downloads Report | Download Stats |