rfPred
This is the development version of rfPred; for the stable release version, see rfPred.
Assign rfPred functional prediction scores to a missense variants list
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.51.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | GPL (>=2 ) |
| Depends | R (>= 3.5.0), methods |
| Imports | utils, Seqinfo, data.table, IRanges, GenomicRanges, parallel, Rsamtools |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rfPred_1.51.0.tar.gz |
| Windows Binary (x86_64) | rfPred_1.51.0.zip |
| macOS Binary (big-sur-x86_64) | rfPred_1.51.0.tgz |
| macOS Binary (sonoma-arm64) | rfPred_1.51.0.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 |