# Transform public data resources into Bioconductor Data Structures

## Documentation for package ‘AnnotationHubData’ version 1.20.1

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

## Help Pages

AnnotationHubData-package | Transform public data resources into Bioconductor Data Structures
AnnotationHubRecipes-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
checkSpeciesTaxId | ValidationFunctions
class:AnnotationHubMetadata | Class '"AnnotationHubMetadata"' and methods
class:HubMetadata | Class '"AnnotationHubMetadata"' and methods
constructSeqInfo | Class '"AnnotationHubMetadata"' and methods
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_S3 | Upload a file to Amazon S3
validationFunctions | ValidationFunctions
validDispatchClass | ValidationFunctions
validSpecies | ValidationFunctions