Package: AnnotationHubData 1.37.0

Bioconductor Package Maintainer

AnnotationHubData: Transform public data resources into Bioconductor Data Structures

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

Authors:Martin Morgan [ctb], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Paul Shannon [ctb], Lori Shepherd [ctb], Bioconductor Package Maintainer [cre]

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AnnotationHubData.pdf |AnnotationHubData.html✨
AnnotationHubData/json (API)
NEWS

# Install 'AnnotationHubData' in R:
install.packages('AnnotationHubData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:AnnotationHubData-1.35.0(bioc 3.20)AnnotationHubData-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.

dataimport

4.88 score 3 packages 21 scripts 814 downloads 46 exports 114 dependencies

Last updated 23 days agofrom:1e4d2394c8. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:ahmToJsonAnnotationHubMetadataannotationHubRootcheckSpeciesTaxIdconstructSeqInfodeleteResourcesensemblFastaToFaFileensemblFastaToTwoBitFilefloggencodeFastaToFaFilegetImportPreparerClassesgetSpeciesListgetValidSourceTypeshubErrorhubError<-HubMetadataFromJsoninputFilesmakeAnnotationHubMetadatamakeAnnotationHubResourcemakeEnsemblFastaToAHMmakeEnsemblTwoBitToAHMmakeGencodeFastaToAHMmakeNCBIToOrgDbsToAHMmakeStandardOrgDbsToAHMmakeStandardTxDbsToAHMmetadatametadata<-metadataListmetadataTablenewResourcesoutputFilepushMetadatapushResourcesrecipeNamerunrunRecipesshowsourceUrlssuggestSpeciestoJsonUCSCTrackImportPreparerupdateResourcesupload_to_azureupload_to_S3validDispatchClassvalidSpecies

Dependencies:abindAnnotationDbiAnnotationForgeAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocCheckBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiocViewsbiomaRtBiostringsbitbit64bitopsblobcachemcallrclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrevaluatefansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhighrhmshttrhttr2IRangesjsonliteKEGGRESTknitrlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslOrganismDbipillarpkgconfigplogrpngprettyunitsprocessxprogresspspurrrR6rappdirsRBGLRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerRUnitrvestS4ArraysS4VectorsselectrsnowSparseArraystringdiststringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrswithrxfunXMLxml2XVectoryamlzlibbioc

Introduction to AnnotationHubData

Lori Shepherd

Rendered fromIntroductionToAnnotationHubData.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-09-10
Started: 2016-08-10

Readme and manuals

Help Manual

Help pageTopics
Transform public data resources into Bioconductor Data StructuresAnnotationHubData-package AnnotationHubRecipes
Class '"AnnotationHubMetadata"' and methodsahmToJson AnnotationHubMetadata AnnotationHubMetadata-class class:AnnotationHubMetadata class:HubMetadata constructSeqInfo deleteResources getImportPreparerClasses hubError hubError,HubMetadata-method hubError,list-method hubError<- hubError<-,HubMetadata,character-method hubError<-,list,character-method HubMetadata HubMetadata-class HubMetadataFromJson inputFiles inputFiles,HubMetadata-method makeAnnotationHubResource metadata metadata,HubMetadata-method metadata<- metadata<-,HubMetadata,list-method outputFile outputFile,HubMetadata-method recipeName recipeName,HubMetadata-method run run,AnnotationHubMetadata-method show show,HubMetadata-method toJson
flogflog
Class 'ImportPreparer' and generic 'newResources'annotationHubRoot dbSNPVCFImportPreparer dbSNPVCFImportPreparer-class EncodeImportPreparer EncodeImportPreparer-class EnsemblFastaImportPreparer EnsemblFastaImportPreparer-class EnsemblGtfImportPreparer EnsemblGtfImportPreparer-class getImportPreparer Grasp2ImportPreparer Grasp2ImportPreparer-class HaemCodeImportPreparer HaemCodeImportPreparer-class ImportPreparer-class Inparanoid8ImportPreparer Inparanoid8ImportPreparer-class metadataList metadataTable NCBIImportPreparer NCBIImportPreparer-class newResources newResources,dbSNPVCFImportPreparer-method newResources,EncodeImportPreparer-method newResources,EnsemblFastaImportPreparer-method newResources,EnsemblGtfImportPreparer-method newResources,Grasp2ImportPreparer-method newResources,HaemCodeImportPreparer-method newResources,ImportPreparer-method newResources,Inparanoid8ImportPreparer-method newResources,NCBIImportPreparer-method newResources,RefNetImportPreparer-method newResources,UCSCChainPreparer-method newResources,UCSCFullTrackImportPreparer-method newResources,UCSCTrackImportPreparer-method RefNetImportPreparer RefNetImportPreparer-class show,ImportPreparer-method sourceUrls UCSCChainPreparer UCSCChainPreparer-class UCSCTrackImportPreparer UCSCTrackImportPreparer-class
Make AnnotationHubMetadata objects from csv file of metadatamakeAnnotationHubMetadata
Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.ensemblFastaToFaFile ensemblFastaToTwoBitFile makeEnsemblFasta makeEnsemblFastaToAHM makeEnsemblTwoBitToAHM
Recipe to add Gencode FASTA resources to AnnotationHubgencodeFastaToFaFile makeGencodeFasta makeGencodeFastaToAHM
Functions to add OrgDb and TxDb sqlite files to AnnotationHubmakeNCBIToOrgDbsToAHM makeNonStandardOrgDbs makeStandardOrgDbs makeStandardOrgDbsToAHM makeStandardTxDbs makeStandardTxDbsToAHM
updateResourcespushMetadata pushResources runRecipes runRecipes,AnnotationHubMetadata-method updateResources
Upload a file to Microsoft Azure Data LakeAzure AZURE_SAS_URL DataLake upload_to_azure
Upload a file to Amazon S3amazon AWS S3 upload_to_S3
ValidationFunctionscheckSpeciesTaxId getSpeciesList getValidSourceTypes suggestSpecies validationFunctions validDispatchClass validSpecies