Transform public data resources into Bioconductor Data Structures

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Documentation for package ‘AnnotationHubData’ version 1.39.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

AnnotationHubData-package	Transform public data resources into Bioconductor Data Structures
ahmToJson	Class '"AnnotationHubMetadata"' and methods
amazon	Upload a file to Amazon S3
AnnotationHubMetadata	Class '"AnnotationHubMetadata"' and methods
AnnotationHubMetadata-class	Class '"AnnotationHubMetadata"' and methods
AnnotationHubRecipes	Transform public data resources into Bioconductor Data Structures
annotationHubRoot	Class 'ImportPreparer' and generic 'newResources'
AWS	Upload a file to Amazon S3
Azure	Upload a file to Microsoft Azure Data Lake
AZURE_SAS_URL	Upload a file to Microsoft Azure Data Lake
checkSpeciesTaxId	ValidationFunctions
class:AnnotationHubMetadata	Class '"AnnotationHubMetadata"' and methods
class:HubMetadata	Class '"AnnotationHubMetadata"' and methods
constructSeqInfo	Class '"AnnotationHubMetadata"' and methods
DataLake	Upload a file to Microsoft Azure Data Lake
dbSNPVCFImportPreparer	Class 'ImportPreparer' and generic 'newResources'
dbSNPVCFImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
deleteResources	Class '"AnnotationHubMetadata"' and methods
EncodeImportPreparer	Class 'ImportPreparer' and generic 'newResources'
EncodeImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
EnsemblFastaImportPreparer	Class 'ImportPreparer' and generic 'newResources'
EnsemblFastaImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
ensemblFastaToFaFile	Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.
ensemblFastaToTwoBitFile	Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.
EnsemblGtfImportPreparer	Class 'ImportPreparer' and generic 'newResources'
EnsemblGtfImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
flog	flog
gencodeFastaToFaFile	Recipe to add Gencode FASTA resources to AnnotationHub
getImportPreparer	Class 'ImportPreparer' and generic 'newResources'
getImportPreparerClasses	Class '"AnnotationHubMetadata"' and methods
getSpeciesList	ValidationFunctions
getValidSourceTypes	ValidationFunctions
Grasp2ImportPreparer	Class 'ImportPreparer' and generic 'newResources'
Grasp2ImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
HaemCodeImportPreparer	Class 'ImportPreparer' and generic 'newResources'
HaemCodeImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
hubError	Class '"AnnotationHubMetadata"' and methods
hubError-method	Class '"AnnotationHubMetadata"' and methods
hubError<-	Class '"AnnotationHubMetadata"' and methods
hubError<--method	Class '"AnnotationHubMetadata"' and methods
HubMetadata	Class '"AnnotationHubMetadata"' and methods
HubMetadata-class	Class '"AnnotationHubMetadata"' and methods
HubMetadataFromJson	Class '"AnnotationHubMetadata"' and methods
ImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
Inparanoid8ImportPreparer	Class 'ImportPreparer' and generic 'newResources'
Inparanoid8ImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
inputFiles	Class '"AnnotationHubMetadata"' and methods
inputFiles-method	Class '"AnnotationHubMetadata"' and methods
makeAnnotationHubMetadata	Make AnnotationHubMetadata objects from csv file of metadata
makeAnnotationHubResource	Class '"AnnotationHubMetadata"' and methods
makeEnsemblFasta	Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.
makeEnsemblFastaToAHM	Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.
makeEnsemblTwoBitToAHM	Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.
makeGencodeFasta	Recipe to add Gencode FASTA resources to AnnotationHub
makeGencodeFastaToAHM	Recipe to add Gencode FASTA resources to AnnotationHub
makeNCBIToOrgDbsToAHM	Functions to add OrgDb and TxDb sqlite files to AnnotationHub
makeNonStandardOrgDbs	Functions to add OrgDb and TxDb sqlite files to AnnotationHub
makeStandardOrgDbs	Functions to add OrgDb and TxDb sqlite files to AnnotationHub
makeStandardOrgDbsToAHM	Functions to add OrgDb and TxDb sqlite files to AnnotationHub
makeStandardTxDbs	Functions to add OrgDb and TxDb sqlite files to AnnotationHub
makeStandardTxDbsToAHM	Functions to add OrgDb and TxDb sqlite files to AnnotationHub
metadata	Class '"AnnotationHubMetadata"' and methods
metadata-method	Class '"AnnotationHubMetadata"' and methods
metadata<-	Class '"AnnotationHubMetadata"' and methods
metadata<--method	Class '"AnnotationHubMetadata"' and methods
metadataList	Class 'ImportPreparer' and generic 'newResources'
metadataTable	Class 'ImportPreparer' and generic 'newResources'
NCBIImportPreparer	Class 'ImportPreparer' and generic 'newResources'
NCBIImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
newResources	Class 'ImportPreparer' and generic 'newResources'
newResources-method	Class 'ImportPreparer' and generic 'newResources'
outputFile	Class '"AnnotationHubMetadata"' and methods
outputFile-method	Class '"AnnotationHubMetadata"' and methods
pushMetadata	updateResources
pushResources	updateResources
recipeName	Class '"AnnotationHubMetadata"' and methods
recipeName-method	Class '"AnnotationHubMetadata"' and methods
RefNetImportPreparer	Class 'ImportPreparer' and generic 'newResources'
RefNetImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
run	Class '"AnnotationHubMetadata"' and methods
run-method	Class '"AnnotationHubMetadata"' and methods
runRecipes	updateResources
runRecipes-method	updateResources
S3	Upload a file to Amazon S3
show	Class '"AnnotationHubMetadata"' and methods
show-method	Class '"AnnotationHubMetadata"' and methods
show-method	Class 'ImportPreparer' and generic 'newResources'
sourceUrls	Class 'ImportPreparer' and generic 'newResources'
suggestSpecies	ValidationFunctions
toJson	Class '"AnnotationHubMetadata"' and methods
UCSCChainPreparer	Class 'ImportPreparer' and generic 'newResources'
UCSCChainPreparer-class	Class 'ImportPreparer' and generic 'newResources'
UCSCTrackImportPreparer	Class 'ImportPreparer' and generic 'newResources'
UCSCTrackImportPreparer-class	Class 'ImportPreparer' and generic 'newResources'
updateResources	updateResources
upload_to_azure	Upload a file to Microsoft Azure Data Lake
upload_to_S3	Upload a file to Amazon S3
validationFunctions	ValidationFunctions
validDispatchClass	ValidationFunctions
validSpecies	ValidationFunctions