rfPred
Assign rfPred functional prediction scores to a missense variants list
Bioconductor version: Release (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>
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
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 |
| Linking To | |
| Suggests | BiocStyle |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_1.38.0.tar.gz |
| Windows Binary | rfPred_1.38.0.zip (64-bit only) |
| 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 |