rfPred

Assign rfPred functional prediction scores to a missense variants list

Bioconductor version: Development (3.0)

Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to be connected on the Internet or to download the TabixFile and index (approximately 3.3 Go).

Author: Fabienne Jabot-Hanin, Hugo Varet and Jean-Philippe Jais

Maintainer: Hugo Varet <varethugo at gmail.com>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("rfPred")

Citation (from within R, enter citation("rfPred")):

Documentation

PDF R Script CalculatingrfPredscoreswithpackagerfPred
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Classification, Software
Version 1.3.1
In Bioconductor since BioC 2.13 (R-3.0)
License GPL (>=2 )
Depends Rsamtools, GenomicRanges, IRanges, data.table, methods, parallel
Imports
Suggests BiocStyle
System Requirements
URL http://www.sbim.fr/rfPred
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source rfPred_1.3.1.tar.gz
Windows Binary rfPred_1.3.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) rfPred_1.3.1.tgz
Mac OS X 10.9 (Mavericks) rfPred_1.3.1.tgz
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