rfPred

DOI: 10.18129/B9.bioc.rfPred    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see rfPred.

Assign rfPred functional prediction scores to a missense variants list

Bioconductor version: 3.8

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>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("rfPred")

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("rfPred")

 

PDF R Script CalculatingrfPredscoreswithpackagerfPred
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Classification, Software
Version 1.20.0
In Bioconductor since BioC 2.13 (R-3.0) (5.5 years)
License GPL (>=2 )
Depends Rsamtools, GenomicRanges, IRanges, data.table, methods, parallel
Imports
LinkingTo
Suggests BiocStyle
SystemRequirements
Enhances
URL http://www.sbim.fr/rfPred
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package rfPred_1.20.0.tar.gz
Windows Binary rfPred_1.20.0.zip
Mac OS X 10.11 (El Capitan) rfPred_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rfPred
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rfPred
Package Short Url http://bioconductor.org/packages/rfPred/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: