DOI: 10.18129/B9.bioc.csaw    

This is the development version of csaw; to use it, please install the devel version of Bioconductor.

ChIP-Seq Analysis with Windows

Bioconductor version: Development (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")):


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biocViews Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.19.0
In Bioconductor since BioC 3.0 (R-3.1) (4.5 years)
License GPL-3
Depends GenomicRanges, SummarizedExperiment
Imports Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, utils
LinkingTo Rhtslib, zlibbioc, Rcpp
Suggests org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
SystemRequirements C++11
Depends On Me
Imports Me diffHic, icetea, NADfinder, vulcan
Suggests Me chipseqDB, csawUsersGuide
Links To Me
Build Report  

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Source Package csaw_1.19.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) csaw_1.19.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/csaw
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/csaw
Package Short Url http://bioconductor.org/packages/csaw/
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