gcapc
GC Aware Peak Caller
Bioconductor version: Release (3.19)
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 "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, ChIPSeq, PeakDetection, Sequencing, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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 |
| System Requirements | |
| URL | https://github.com/tengmx/gcapc |
See More
| Suggests | BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | epigraHMM |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gcapc_1.28.0.tar.gz |
| Windows Binary (x86_64) | gcapc_1.28.0.zip |
| macOS Binary (x86_64) | gcapc_1.28.0.tgz |
| macOS Binary (arm64) | gcapc_1.28.0.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 |