DOI: 10.18129/B9.bioc.gcapc    

This is the development version of gcapc; for the stable release version, see gcapc.

GC Aware Peak Caller

Bioconductor version: Development (3.7)

Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

Author: Mingxiang Teng and Rafael A. Irizarry

Maintainer: Mingxiang Teng <tengmx at gmail.com>

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biocViews BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software
Version 1.3.0
In Bioconductor since BioC 3.5 (R-3.4) (1 year)
License GPL-3
Depends R (>= 3.4)
Imports BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods
Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
URL https://github.com/tengmx/gcapc
Depends On Me
Imports Me
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Source Package gcapc_1.3.0.tar.gz
Windows Binary gcapc_1.3.0.zip
Mac OS X 10.11 (El Capitan) gcapc_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gcapc
Package Short Url http://bioconductor.org/packages/gcapc/
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