csaw
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see csaw.
ChIP-Seq Analysis with Windows
Bioconductor version: 3.10
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 "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.20.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL-3 |
| Depends | GenomicRanges, SummarizedExperiment |
| Imports | Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, utils |
| System Requirements | C++11, GNU make |
| URL |
See More
| Suggests | org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager |
| Linking To | Rhtslib, zlibbioc, Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | diffHic, icetea, NADfinder, vulcan |
| Suggests Me | chipseqDB, csawUsersGuide, tximport |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | csaw_1.20.0.tar.gz |
| Windows Binary | csaw_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | csaw_1.20.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |