gcapc

DOI: 10.18129/B9.bioc.gcapc    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see gcapc.

GC Aware Peak Caller

Bioconductor version: 3.14

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 (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gcapc")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("gcapc")

 

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

Details

biocViews	BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 3.5 (R-3.4) (5 years)
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	epigraHMM
Links To Me
Build Report

Package Archives

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

Source Package	gcapc_1.18.0.tar.gz
Windows Binary	gcapc_1.18.0.zip
macOS 10.13 (High Sierra)	gcapc_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gcapc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gcapc
Package Short Url	https://bioconductor.org/packages/gcapc/
Package Downloads Report	Download Stats