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rfPred

Assign rfPred functional prediction scores to a missense variants list


Bioconductor version: Release (3.18)

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>

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

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")
CalculatingrfPredscoreswithpackagerfPred PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Classification, Software
Version 1.40.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL (>=2 )
Depends R (>= 3.5.0), methods
Imports utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools
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Package Archives

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

Source Package rfPred_1.40.0.tar.gz
Windows Binary rfPred_1.40.0.zip
macOS Binary (x86_64) rfPred_1.40.0.tgz
macOS Binary (arm64) rfPred_1.40.0.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/
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