Package: myvariant 1.37.0
Adam Mark, Chunlei Wu
myvariant: Accesses MyVariant.info variant query and annotation services
MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services
Authors:
myvariant_1.37.0.tar.gz
myvariant_1.37.0.zip(r-4.5)myvariant_1.37.0.zip(r-4.4)myvariant_1.37.0.zip(r-4.3)
myvariant_1.37.0.tgz(r-4.4-any)myvariant_1.37.0.tgz(r-4.3-any)
myvariant_1.37.0.tar.gz(r-4.5-noble)myvariant_1.37.0.tar.gz(r-4.4-noble)
myvariant_1.37.0.tgz(r-4.4-emscripten)myvariant_1.37.0.tgz(r-4.3-emscripten)
myvariant.pdf |myvariant.html✨
myvariant/json (API)
| # Install 'myvariant' in R: |
| install.packages('myvariant', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:myvariant-1.35.0(bioc 3.20)myvariant-1.34.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
variantannotationannotationgenomicvariation
Last updated 23 days agofrom:ef53b5c1aa. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:formatHgvsformatSingleHgvsgetVariantgetVariantsmetadataMyVariantqueryVariantqueryVariants
Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydigestevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get all HGVS IDs from Vcf object. | formatHgvs |
| Get Hgvs HGVS ID from chromosome, position, reference and alternate alleles. | formatSingleHgvs |
| Return the variant object for the given HGVS id. | getVariant getVariant,missing-method getVariant,MyVariant-method |
| Return the list of variant objects for the given list of HGVS ids. | getVariants getVariants,missing-method getVariants,MyVariant-method |
| metadata | metadata metadata,MyVariant-method |
| Access MyVariant.info variant annotation services | myvariant |
| MyVariant | MyVariant |
| Class '"MyVariant"' | MyVariant-class |
| Return the query result. | queryVariant queryVariant,missing-method queryVariant,MyVariant-method |
| Return the batch query result. | queryVariants queryVariants,missing-method queryVariants,MyVariant-method |
