To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gcapc")
In most cases, you don't need to download the package archive at all.
gcapc
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GC Aware Peak Caller
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gcapc")
Documentation
| HTML | R Script | The gcapc user's guide |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software |
| Version | 1.0.9 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gcapc_1.0.9.tar.gz |
| Windows Binary | gcapc_1.0.9.zip |
| Mac OS X 10.11 (El Capitan) | gcapc_1.0.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gcapc |
| Package Short Url | http://bioconductor.org/packages/gcapc/ |
| Package Downloads Report | Download Stats |
Documentation »
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