rfPred: Assign rfPred functional prediction scores to a missense variants list

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rfPred")
AuthorFabienne Jabot-Hanin, Hugo Varet and Jean-Philippe Jais
Bioconductor views Annotation Classification Software
Date of publicationNone
MaintainerHugo Varet <varethugo@gmail.com>
LicenseGPL (>=2 )
Version1.14.0
http://www.sbim.fr/rfPred

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/NAMESPACE.r R/example_GRanges.r R/rfPred-package.r R/rfPred_scores-methods.r R/rfPred_scores_motor.r R/variant_list_Y.r
build
build/vignette.rds
data
data/example_GRanges.rda
data/variant_list_Y.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/extdata
inst/extdata/chrY_rfPred.txtz
inst/extdata/chrY_rfPred.txtz.tbi
inst/extdata/example.vcf
man
man/example_GRanges.Rd man/rfPred-package.Rd man/rfPred_scores-methods.Rd man/rfPred_scores_motor.Rd man/variant_list_Y.Rd
src
src/outstring.c
vignettes
vignettes/vignette.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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