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cn.farms

This is the development version of cn.farms; for the stable release version, see cn.farms.

cn.FARMS - factor analysis for copy number estimation


Bioconductor version: Development (3.19)

This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.

Author: Andreas Mitterecker, Djork-Arne Clevert

Maintainer: Andreas Mitterecker <mitterecker at ml.jku.at>

Citation (from within R, enter citation("cn.farms")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("cn.farms")

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("cn.farms")
cn.farms: Manual for the R package PDF R Script
Reference Manual PDF

Details

biocViews CopyNumberVariation, Microarray, Software
Version 1.51.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License LGPL (>= 2.0)
Depends R (>= 3.0), Biobase, methods, ff, oligoClasses, snow
Imports DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
System Requirements
URL http://www.bioinf.jku.at/software/cnfarms/cnfarms.html
See More
Suggests pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cn.farms_1.51.0.tar.gz
Windows Binary cn.farms_1.51.0.zip
macOS Binary (x86_64) cn.farms_1.51.0.tgz
macOS Binary (arm64) cn.farms_1.51.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cn.farms
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cn.farms
Bioc Package Browser https://code.bioconductor.org/browse/cn.farms/
Package Short Url https://bioconductor.org/packages/cn.farms/
Package Downloads Report Download Stats