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biocLite("cn.farms")
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cn.farms
cn.FARMS - factor analysis for copy number estimation
Bioconductor version: 3.0
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 bioinf.jku.at>
Citation (from within R,
enter citation("cn.farms")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("cn.farms")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cn.farms")
| R Script | cn.farms: Manual for the R package | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Microarray, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| License | LGPL (>= 2.0) |
| Depends | R (>= 3.0), Biobase, methods, ff, oligoClasses, snow |
| Imports | DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice |
| LinkingTo | |
| Suggests | pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 |
| SystemRequirements | |
| Enhances | |
| URL | http://www.bioinf.jku.at/software/cnfarms/cnfarms.html |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | cn.farms_1.14.0.tar.gz |
| Windows Binary | cn.farms_1.14.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | cn.farms_1.14.0.tgz |
| Mac OS X 10.9 (Mavericks) | cn.farms_1.14.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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