gcapc

DOI: 10.18129/B9.bioc.gcapc    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see gcapc.

GC Aware Peak Caller

Bioconductor version: 3.15

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 "4.2") 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 1.20.0
In Bioconductor since BioC 3.5 (R-3.4) (5.5 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_1.20.0.tar.gz
Windows Binary gcapc_1.20.0.zip (64-bit only)
macOS Binary (x86_64) gcapc_1.20.0.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

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