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Bioconductor - gcapc

gcapc

This is the released version of gcapc; for the devel version, see gcapc.

GC Aware Peak Caller

Bioconductor version: Release (3.21)

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 "4.5") 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")
Details biocViews BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software Version 1.32.0 In Bioconductor since BioC 3.5 (R-3.4) (8 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 Package Archives

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

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