csaw
ChIP-Seq Analysis with Windows
Bioconductor version: Release (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")
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 | 1.40.0 |
| 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_1.40.0.tar.gz |
| Windows Binary (x86_64) | csaw_1.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | csaw_1.40.0.tgz |
| macOS Binary (arm64) | csaw_1.40.0.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 |