gcapc

DOI: 10.18129/B9.bioc.gcapc    

GC Aware Peak Caller

Bioconductor version: Release (3.6)

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>

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	1.2.0
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
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.

Source Package	gcapc_1.2.0.tar.gz
Windows Binary	gcapc_1.2.0.zip
Mac OS X 10.11 (El Capitan)	gcapc_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gcapc
Package Short Url	http://bioconductor.org/packages/gcapc/
Package Downloads Report	Download Stats