Package: rfPred 1.50.0
Hugo Varet
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 download the TabixFile and index (approximately 3.3 Go).
Authors:
rfPred_1.50.0.tar.gz
rfPred_1.50.0.zip(r-4.7)rfPred_1.50.0.zip(r-4.6)rfPred_1.50.0.zip(r-4.5)
rfPred_1.50.0.tgz(r-4.6-x86_64)rfPred_1.50.0.tgz(r-4.6-arm64)rfPred_1.50.0.tgz(r-4.5-x86_64)rfPred_1.50.0.tgz(r-4.5-arm64)
rfPred_1.50.0.tar.gz(r-4.7-arm64)rfPred_1.50.0.tar.gz(r-4.7-x86_64)rfPred_1.50.0.tar.gz(r-4.6-arm64)rfPred_1.50.0.tar.gz(r-4.6-x86_64)
rfPred_1.50.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rfPred/json (API)
NEWS
| # Install 'rfPred' in R: |
| install.packages('rfPred', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
- example_GRanges - Toy example of GRanges object
- variant_list_Y - Toy example of data.frame
On BioConductor:rfPred-1.51.0(bioc 3.24)rfPred-1.50.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwareannotationclassification
Last updated from:8ef11e927c (on RELEASE_3_23). Checks:1 ERROR, 13 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 184 | ||
| linux-devel-arm64 | OK | 196 | ||
| linux-devel-x86_64 | OK | 240 | ||
| source / vignettes | OK | 250 | ||
| linux-release-arm64 | OK | 186 | ||
| linux-release-x86_64 | OK | 225 | ||
| macos-release-arm64 | OK | 143 | ||
| macos-release-x86_64 | OK | 411 | ||
| macos-oldrel-arm64 | OK | 97 | ||
| macos-oldrel-x86_64 | OK | 320 | ||
| windows-devel | OK | 177 | ||
| windows-release | OK | 129 | ||
| windows-oldrel | OK | 141 | ||
| wasm-release | OK | 121 |
Exports:rfPred_scoresrfPred_scores_motor
Dependencies:BHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayondata.tableformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rRhtslibRsamtoolsS4VectorsSeqinfosnowXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assign functional prediction rfPred scores to human missense variants (random forest method based on SIFT, Polyphen2, PhyloP, LRT and Mutation Taster) | rfPred-package rfPred |
| Toy example of GRanges object | example_GRanges |
| Assign functional prediction rfPred scores to human missense variants | rfPred_scores rfPred_scores,character-method rfPred_scores,data.frame-method rfPred_scores,GRanges-method |
| Motor of 'rfPred_scores' | rfPred_scores_motor |
| Toy example of data.frame | variant_list_Y |
