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gcapc

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

GC Aware Peak Caller

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.25.0
In Bioconductor since BioC 3.5 (R-3.4) (6.5 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
Linking To
Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
System Requirements
Enhances
URL https://github.com/tengmx/gcapc
See More
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_1.25.0.tar.gz
Windows Binary gcapc_1.25.0.zip
macOS Binary (x86_64) gcapc_1.25.0.tgz
macOS Binary (arm64) gcapc_1.25.0.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