AnnotationHubData
Transform public data resources into Bioconductor Data Structures

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Functions
276
Source code
38
Man pages
11
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AnnotationHubData: Transform public data resources into Bioconductor Data Structures
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API

API for AnnotationHubData
Transform public data resources into Bioconductor Data Structures

Global functions
.EpiFilesDescription Source code
.EpiFilesMetadata Source code
.EpiFilesTags Source code
.EpiMetadataFile Source code
.MiscEpiFiles Source code
.NCBIMetadataFromUrl Source code
.TxDbPkgMetadataFromObjs Source code
.UCSCTrackMetadata Source code
.UCSCTrackSourceTracks Source code
.ValidHubs Source code
.allMajorTablesSQL Source code
.cachedTracks Source code
.checkAllTracks Source code
.checkFileLengths Source code
.checkRDataClassConsistent Source code
.checkRdataclassIsReal Source code
.checkSourceurlPrefixesAreValid Source code
.checkSourceurlsFreeOfDoubleSlashes Source code
.checkThatGenomeLooksReasonable Source code
.checkThatRDataPathIsOK Source code
.checkThatSingleStringAndNoCommas Source code
.checkThatSingleStringOrNA Source code
.checkThatSingleStringOrNAAndNoCommas Source code
.checkThatSourceTypeSoundsReasonable Source code
.checkValidMaintainer Source code
.checkValidSingleString Source code
.chmmModels Source code
.cleanFiles Source code
.cleanOneTable Source code
.compressTable Source code
.decodeNA Source code
.derivedFileName Source code
.dnaMethylation Source code
.encodeFiles Source code
.encodeNA Source code
.ensemblDirUrl Source code
.ensemblFastaSourceUrls Source code
.ensemblGtfSourceUrls Source code
.ensemblMetadataFromUrl Source code
.expandLine Source code
.expressionAnnotationGtf Source code
.expressionTextFiles Source code
.fastaToFaFile Source code
.filter Source code
.findBadTracks Source code
.findTrackTables Source code
.ftpDirectoryInfo Source code
.ftpFileInfo Source code
.gencodeDescription Source code
.gencodeFileFromUrl Source code
.gencodeGenome Source code
.gencodeSourceUrls Source code
.generalNewResources Source code
.getAllBreakPoints Source code
.getAnnotHubCon Source code
.getBadTracksForGenomes Source code
.getDuplicatedRowIds Source code
.getGenomeAbbrevs Source code
.getHaemCode Source code
.getHaemCodeFileNames Source code
.getLatestTrackDate Source code
.getListing Source code
.getMergeArgs Source code
.getNamedGenomeBreakPoints Source code
.getOrgDbs Source code
.getOtherTableDupIDs Source code
.getRefNetFileURIs Source code
.getTableDates Source code
.getTags Source code
.getTrackTablesForAllGenomes Source code
.getTrackTablesForGenome Source code
.getTracksForGenomes Source code
.getTxDbs Source code
.getUCSCResources Source code
.getchainFiles Source code
.getdbSNP Source code
.httrFileInfo Source code
.httrRead Source code
.inparanoidMetadataFromUrl Source code
.isComplete Source code
.listRemoteFiles Source code
.makeAuxTable Source code
.makeComplexGR Source code
.makeEpigenomeRoadmap Source code
.onLoad Source code
.orgDbPkgMetadataFromObjs Source code
.organismToTaxid Source code
.parseDirInfo Source code
.peakEpiFiles Source code
.printf Source code
.readEpiFilesFromWebUrl Source code
.readHTMLTable Source code
.readMetadataFromCsv Source code
.refnetFiles Source code
.removeId Source code
.removeOneRecord Source code
.signalEpiFiles Source code
.sortTableByChromosomalLocation Source code
.subDir Source code
AWS Man page
AnnotationHubData-package Man page
AnnotationHubMetadata Man page Man page Source code
AnnotationHubMetadata-class Man page
AnnotationHubRecipes Man page
AnnotationHubRecipes-package Man page
EncodeImportPreparer Man page
EncodeImportPreparer-class Man page
EnsemblFastaImportPreparer Man page
EnsemblFastaImportPreparer-class Man page
EnsemblGtfImportPreparer Man page
EnsemblGtfImportPreparer-class Man page
Grasp2ImportPreparer Man page
Grasp2ImportPreparer-class Man page
HaemCodeImportPreparer Man page
HaemCodeImportPreparer-class Man page
HubMetadata Man page
HubMetadata-class Man page
HubMetadataFromJson Man page Source code
ImportPreparer-class Man page
Inparanoid8ImportPreparer Man page
Inparanoid8ImportPreparer-class Man page
NCBIImportPreparer Man page
NCBIImportPreparer-class Man page
NCBIToOrgDbs Source code
RefNetImportPreparer Man page
RefNetImportPreparer-class Man page
S3 Man page
UCSCChainPreparer Man page
UCSCChainPreparer-class Man page
UCSCTrackImportPreparer Man page
UCSCTrackImportPreparer-class Man page
URL_parts Source code
`%_%` Source code
`deref<-` Source code
ahmToJson Man page Source code
amazon Man page
annotationHubRoot Man page
as.pointer Source code
checkSpeciesTaxId Man page Source code
class:AnnotationHubMetadata Man page
class:HubMetadata Man page
cleanupLst Source code
constructSeqInfo Man page Source code
dbSNPVCFImportPreparer Man page
dbSNPVCFImportPreparer-class Man page
deleteResources Man page Source code
deref Source code
downloadResource Source code
ensemblFastaToFaFile Man page Source code
ensemblFastaToTwoBitFile Man page Source code
extractOrgDbSqlite Source code
extractTxDbSqlite Source code
flog Man page Source code
gencodeFastaToFaFile Man page Source code
gencodeGFFToGRanges Source code
getCurrentResources Source code
getImportPreparer Man page
getImportPreparerClasses Man page Source code
getLatestTableDates Source code
getLatestTrackDates Source code
getSpeciesList Man page Source code
getValidSourceTypes Man page Source code
hubError Man page
hubError,HubMetadata-method Man page
hubError,list-method Man page
hubError<- Man page
hubError<-,HubMetadata,character-method Man page
hubError<-,list,character-method Man page
inparanoid8ToDbsRecipe Source code
inputFiles Man page
inputFiles,HubMetadata-method Man page
is.pointer Source code
make2bit Source code
makeAnnotationHubMetadata Man page Source code
makeAnnotationHubResource Man page Source code
makeChEAToAHM Source code
makeEncodeImporter Source code
makeEnsemblFasta Man page
makeEnsemblFastaToAHM Man page Source code
makeEnsemblGtfToAHM Source code
makeEnsemblTwoBitToAHM Man page Source code
makeEpigenomeRoadmap Source code
makeEpigenomeRoadmapPeak Source code
makeGencodeFasta Man page
makeGencodeFastaToAHM Man page Source code
makeGencodeGFFsToAHMs Source code
makeHaemCodeImporter Source code
makeNCBIToOrgDbsToAHM Man page Source code
makeNonStandardOrgDbs Man page
makeRefNetImporter Source code
makeStandardOrgDbs Man page
makeStandardOrgDbsToAHM Man page Source code
makeStandardTxDbs Man page
makeStandardTxDbsToAHM Man page Source code
makeUCSCChain Source code
makedbSNPVCF Source code
makeinparanoid8ToAHMs Source code
metadata Man page
metadata,HubMetadata-method Man page
metadata<- Man page
metadata<-,HubMetadata,list-method Man page
metadataList Man page
metadataTable Man page
ncbi_dbSNPVCFFile Source code
needToRerunNonStandardOrgDb Source code
newResources Man page
newResources,EncodeImportPreparer-method Man page
newResources,EnsemblFastaImportPreparer-method Man page
newResources,EnsemblGtfImportPreparer-method Man page
newResources,Grasp2ImportPreparer-method Man page
newResources,HaemCodeImportPreparer-method Man page
newResources,ImportPreparer-method Man page
newResources,Inparanoid8ImportPreparer-method Man page
newResources,NCBIImportPreparer-method Man page
newResources,RefNetImportPreparer-method Man page
newResources,UCSCChainPreparer-method Man page
newResources,UCSCFullTrackImportPreparer-method Man page
newResources,UCSCTrackImportPreparer-method Man page
newResources,dbSNPVCFImportPreparer-method Man page
outputFile Man page
outputFile,HubMetadata-method Man page
pointer Source code
print.pointer Source code
pushMetadata Man page Source code
pushResources Man page Source code
recipeName Man page
recipeName,HubMetadata-method Man page
run Man page
run,AnnotationHubMetadata-method Man page
runRecipes Man page
runRecipes,AnnotationHubMetadata-method Man page
show Man page
show,HubMetadata-method Man page
show,ImportPreparer-method Man page
sourceUrls Man page
suggestSpecies Man page Source code
toJson Man page Source code
trackToGRangesRecipe Source code
trackWithAuxiliaryTablesToGRanges Source code
trackandTablesToGRangesRecipe Source code
updateResources Man page Source code
upload_to_S3 Man page Source code
validDispatchClass Man page Source code
validSpecies Man page Source code
validationFunctions Man page
writeJSON Source code
AnnotationHubData documentation built on April 17, 2021, 6:05 p.m.

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