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")

The gcapc user's guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software

Version 1.20.0

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

Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10

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Build Report 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

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 3.15 Source Archive