DOI: 10.18129/B9.bioc.gcapc  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see gcapc.

GC Aware Peak Caller

Bioconductor version: 3.16

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")):


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biocViews BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 3.5 (R-3.4) (6 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
Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
URL https://github.com/tengmx/gcapc
Depends On Me
Imports Me
Suggests Me epigraHMM
Links To Me
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Source Package gcapc_1.22.0.tar.gz
Windows Binary gcapc_1.22.0.zip (64-bit only)
macOS Binary (x86_64) gcapc_1.22.0.tgz
macOS Binary (arm64) gcapc_1.22.0.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/
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