HMMcopy
This is the development version of HMMcopy; for the stable release version, see HMMcopy.
Copy number prediction with correction for GC and mappability bias for HTS data
Bioconductor version: Development (3.24)
Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.
Author: Daniel Lai, Gavin Ha, Sohrab Shah
Maintainer: Andrew McPherson <andrew.mcpherson at gmail.com>
citation("HMMcopy")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("HMMcopy")
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("HMMcopy")| HMMcopy | R Script | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization |
| Version | 1.55.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 years) |
| License | GPL-3 |
| Depends | R (>= 2.10.0), data.table (>= 1.11.8) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | qsea |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HMMcopy_1.55.1.tar.gz |
| Windows Binary (x86_64) | HMMcopy_1.55.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HMMcopy_1.55.1.tgz |
| macOS Binary (sonoma-arm64) | HMMcopy_1.55.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HMMcopy |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HMMcopy |
| Bioc Package Browser | https://code.bioconductor.org/browse/HMMcopy/ |
| Package Short Url | https://bioconductor.org/packages/HMMcopy/ |
| Package Downloads Report | Download Stats |