1 Overview | 2 Variant Annotation Service | 3 Variant Query Service | 4 References
Package: myvariant 1.43.0
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_1.43.0.tar.gz
myvariant_1.43.0.zip(r-4.7)myvariant_1.43.0.zip(r-4.6)myvariant_1.43.0.zip(r-4.5)
myvariant_1.43.0.tgz(r-4.6-any)myvariant_1.43.0.tgz(r-4.5-any)
myvariant_1.43.0.tar.gz(r-4.7-any)myvariant_1.43.0.tar.gz(r-4.6-any)
myvariant_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.43.0(bioc 3.24)myvariant-1.42.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
variantannotationannotationgenomicvariation
Last updated from:17c248a4a0. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 236 | ||
| linux-devel-x86_64 | NOTE | 441 | ||
| source / vignettes | OK | 336 | ||
| linux-release-x86_64 | NOTE | 453 | ||
| macos-release-arm64 | NOTE | 284 | ||
| macos-oldrel-arm64 | NOTE | 195 | ||
| windows-devel | NOTE | 295 | ||
| windows-release | NOTE | 345 | ||
| windows-oldrel | NOTE | 283 | ||
| wasm-release | OK | 193 |
Exports:formatHgvsformatSingleHgvsgetVariantgetVariantsmetadataMyVariantqueryVariantqueryVariants
Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydigestevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigplyrpngR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml
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 |
