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>

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

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

Details

biocViews BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software
Version 1.18.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
System Requirements
URL https://github.com/tengmx/gcapc
See More
Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me epigraHMM
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/gcapc/
Package Short Url https://bioconductor.org/packages/gcapc/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive