Bioconductor – csaw

 
 

This package is for version 3.2 of Bioconductor;
for the stable, up-to-date release version, see
csaw.

ChIP-seq analysis with windows

Bioconductor version: 3.2

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Author: Aaron Lun <alun at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>

Maintainer: Aaron Lun <alun at wehi.edu.au>

Citation (from within R,
enter citation("csaw")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("csaw")

Documentation

To view documentation for the version of this package installed
in your system, start R and enter:

browseVignettes("csaw")

 

PDF

csaw Vignette

PDF

csawUserGuide.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, ChIPSeq, Coverage, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.4.1
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-3
Depends R (>= 3.2.0), GenomicRanges, SummarizedExperiment
Imports Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, GenomicAlignments, S4Vectors, IRanges, GenomeInfoDb
LinkingTo
Suggests org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me diffHic
Suggests Me
Build Report  

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