HMMcopy
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see HMMcopy.
Copy number prediction with correction for GC and mappability bias for HTS data
Bioconductor version: 3.13
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: Daniel Lai <dalai at bccrc.ca>, Sohrab Shah <shahs3 at mskcc.org>
citation("HMMcopy")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.34.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 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_1.34.0.tar.gz |
| Windows Binary | HMMcopy_1.34.0.zip |
| macOS 10.13 (High Sierra) | HMMcopy_1.34.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |