gcapc
This is the released version of gcapc; for the devel version, see gcapc.
GC Aware Peak Caller
Bioconductor version: Release (3.23)
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("gcapc")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.4) |
| Imports | BiocGenerics, Seqinfo, 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_1.36.0.tar.gz |
| Windows Binary (x86_64) | gcapc_1.36.0.zip |
| macOS Binary (big-sur-x86_64) | gcapc_1.36.0.tgz |
| macOS Binary (sonoma-arm64) | gcapc_1.36.0.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 |