To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

gcapc

 

   

GC Aware Peak Caller

Bioconductor version: Release (3.5)

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>

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

Installation

To install this package, start R and enter:

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

Documentation

HTML R Script The gcapc user's guide
PDF   Reference Manual
Text   NEWS

Details

biocViews BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software
Version 1.0.8
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL-3
Depends R (>= 3.4)
Imports BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
SystemRequirements
Enhances
URL https://github.com/tengmx/gcapc
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source gcapc_1.0.8.tar.gz
Windows Binary gcapc_1.0.8.zip
Mac OS X 10.11 (El Capitan) gcapc_1.0.8.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/gcapc/tree/release-3.5
Package Short Url http://bioconductor.org/packages/gcapc/
Package Downloads Report Download Stats

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