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>

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