rfPred

DOI: 10.18129/B9.bioc.rfPred  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see rfPred.

Assign rfPred functional prediction scores to a missense variants list

Bioconductor version: 3.17

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 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 "4.3") and enter:

if (!require("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	1.38.0
In Bioconductor since	BioC 2.13 (R-3.0) (10 years)
License	GPL (>=2 )
Depends	R (>= 3.5.0), methods
Imports	utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools
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Suggests	BiocStyle
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Package Archives

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

Source Package	rfPred_1.38.0.tar.gz
Windows Binary	rfPred_1.38.0.zip
macOS Binary (x86_64)	rfPred_1.38.0.tgz
macOS Binary (arm64)	rfPred_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rfPred
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rfPred
Bioc Package Browser	https://code.bioconductor.org/browse/rfPred/
Package Short Url	https://bioconductor.org/packages/rfPred/
Package Downloads Report	Download Stats