Transform public data resources into Bioconductor Data Structures


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Documentation for package ‘AnnotationHubData’ version 1.22.0

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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