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.

AuthorMartin Morgan [ctb], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Paul Shannon [ctb], Bioconductor Package Maintainer [cre]
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.4.1

View on Bioconductor

Functions

ahmToJson Man page
amazon Man page
AnnotationHubMetadata Man page
AnnotationHubMetadata Man page
AnnotationHubMetadata-class Man page
AnnotationHubRecipes Man page
AnnotationHubRecipes-package Man page
annotationHubRoot Man page
AWS Man page
class:AnnotationHubMetadata Man page
class:HubMetadata Man page
constructAnnotationHubMetadataFromSourceFilePath Man page
constructMetadataFromJsonPath Man page
constructSeqInfo Man page
dbSNPVCFImportPreparer Man page
dbSNPVCFImportPreparer-class Man page
deleteResources Man page
EncodeImportPreparer Man page
EncodeImportPreparer-class Man page
EnsemblFastaImportPreparer Man page
EnsemblFastaImportPreparer-class Man page
ensemblFastaToFaFile Man page
ensemblFastaToTwoBitFile Man page
EnsemblGtfImportPreparer Man page
EnsemblGtfImportPreparer-class Man page
flog Man page
gencodeFastaToFaFile Man page
getImportPreparer Man page
getImportPreparerClasses Man page
Grasp2ImportPreparer Man page
Grasp2ImportPreparer-class Man page
HaemCodeImportPreparer Man page
HaemCodeImportPreparer-class Man page
hubError Man page
hubError<- Man page
hubError<-,HubMetadata,character-method Man page
hubError,HubMetadata-method Man page
hubError<-,list,character-method Man page
hubError,list-method Man page
HubMetadata Man page
HubMetadata-class Man page
HubMetadataFromJson Man page
ImportPreparer-class Man page
Inparanoid8ImportPreparer Man page
Inparanoid8ImportPreparer-class Man page
inputFiles Man page
inputFiles,HubMetadata-method Man page
jsonPath Man page
makeAnnotationHubMetadata Man page
makeAnnotationHubResource Man page
makeEnsemblFasta Man page
makeEnsemblFastaToAHM Man page
makeEnsemblTwoBitToAHM Man page
makeGencodeFasta Man page
makeGencodeFastaToAHM Man page
metadata Man page
metadata<- Man page
metadata.csv Man page
metadata<-,HubMetadata,list-method Man page
metadata,HubMetadata-method Man page
metadataList Man page
metadataTable Man page
NCBIImportPreparer Man page
NCBIImportPreparer-class Man page
newResources Man page
newResources,dbSNPVCFImportPreparer-method 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
outputFile Man page
outputFile,HubMetadata-method Man page
pushMetadata Man page
pushResources Man page
readMetadataFromCsv Man page
recipeName Man page
recipeName,HubMetadata-method Man page
RefNetImportPreparer Man page
RefNetImportPreparer-class Man page
run Man page
run,AnnotationHubMetadata-method Man page
runRecipes Man page
runRecipes,AnnotationHubMetadata-method Man page
S3 Man page
show Man page
show,HubMetadata-method Man page
show,ImportPreparer-method Man page
sourceUrls Man page
toJson Man page
UCSCChainPreparer Man page
UCSCChainPreparer-class Man page
UCSCTrackImportPreparer Man page
UCSCTrackImportPreparer-class Man page
updateResources Man page
upload_to_S3 Man page

Files

AnnotationHubData/DESCRIPTION
AnnotationHubData/NAMESPACE
AnnotationHubData/NEWS
AnnotationHubData/R
AnnotationHubData/R/AnnotationHubMetadata-class.R AnnotationHubData/R/HubMetadata-class.R AnnotationHubData/R/ImportPreparer-class.R AnnotationHubData/R/Message-class.R AnnotationHubData/R/UCSCTrackUpdateChecker.R AnnotationHubData/R/ahmToJson.R AnnotationHubData/R/makeAnnotationHubResource.R AnnotationHubData/R/makeBioPaxImporter.R AnnotationHubData/R/makeChEA.R AnnotationHubData/R/makeEncodeDCC.R AnnotationHubData/R/makeEnsemblFasta.R AnnotationHubData/R/makeEnsemblGtfToGRanges.R AnnotationHubData/R/makeEnsemblTwoBit.R AnnotationHubData/R/makeEpigenomeRoadmap.R AnnotationHubData/R/makeGencodeFasta.R AnnotationHubData/R/makeGencodeGFF.R AnnotationHubData/R/makeGrasp2Db.R AnnotationHubData/R/makeHaemCode.R AnnotationHubData/R/makeInparanoid8ToDbs.R AnnotationHubData/R/makeNCBIToOrgDbs.R AnnotationHubData/R/makePazar.R AnnotationHubData/R/makeRecentOrgPkgsToDbs.R AnnotationHubData/R/makeRefNet.R AnnotationHubData/R/makeUCSC2Bit.R AnnotationHubData/R/makeUCSCChain.R AnnotationHubData/R/makeUCSCTracks.R AnnotationHubData/R/makedbSNPVCF.R AnnotationHubData/R/readMetadataFromCsv.R AnnotationHubData/R/trackWithAuxiliaryTableToGRangesRecipe.R AnnotationHubData/R/updateResources.R AnnotationHubData/R/utils.R AnnotationHubData/R/webAccessFunctions.R
AnnotationHubData/appveyor.yml
AnnotationHubData/build
AnnotationHubData/build/vignette.rds
AnnotationHubData/inst
AnnotationHubData/inst/doc
AnnotationHubData/inst/doc/IntroductionToAnnotationHubData.R
AnnotationHubData/inst/doc/IntroductionToAnnotationHubData.Rmd
AnnotationHubData/inst/doc/IntroductionToAnnotationHubData.html
AnnotationHubData/inst/extdata
AnnotationHubData/inst/extdata/annotation_haemcode.tsv
AnnotationHubData/inst/extdata/badUCSCTracks
AnnotationHubData/inst/extdata/badUCSCTracks/allBadTracks.rda
AnnotationHubData/inst/extdata/badUCSCTracks/allPossibleTracks.rda
AnnotationHubData/inst/extdata/badUCSCTracks/genomeTrackTable.Rda
AnnotationHubData/inst/extdata/haemCodeFileList.txt
AnnotationHubData/inst/extdata/inpDrosPsuedo.rda
AnnotationHubData/inst/makefile
AnnotationHubData/inst/scripts
AnnotationHubData/inst/scripts/communityContributions.R
AnnotationHubData/inst/scripts/createJsonForTesting.R
AnnotationHubData/inst/scripts/oldVignettes
AnnotationHubData/inst/scripts/oldVignettes/AnnotationHubData.Rmd
AnnotationHubData/inst/scripts/oldVignettes/AnnotationHubRecipes.Rmd
AnnotationHubData/inst/unitTests
AnnotationHubData/inst/unitTests/cases
AnnotationHubData/inst/unitTests/cases/encodeDCCMetadata
AnnotationHubData/inst/unitTests/cases/encodeDCCMetadata/downloads
AnnotationHubData/inst/unitTests/cases/encodeDCCMetadata/tbl.parsedEncodeMetadata.RData
AnnotationHubData/inst/unitTests/cases/encodeDCCMetadata/wgEncodeAffyRnaChip.info
AnnotationHubData/inst/unitTests/cases/encodeDCCMetadata/wgEncodeAwgDnaseUniform.info
AnnotationHubData/inst/unitTests/test_AnnotationHubConstructor.R
AnnotationHubData/inst/unitTests/test_ImportPreparer-class.R
AnnotationHubData/inst/unitTests/test_recipe.R
AnnotationHubData/inst/unitTests/test_webAccessFunctions.R
AnnotationHubData/man
AnnotationHubData/man/AnnotationHubData-package.Rd AnnotationHubData/man/AnnotationHubMetadata-class.Rd AnnotationHubData/man/ImportPreparer-class.Rd AnnotationHubData/man/flog.Rd AnnotationHubData/man/makeAnnotationHubMetadata.Rd AnnotationHubData/man/makeEnsemblFasta.Rd AnnotationHubData/man/makeGencodeFasta.Rd AnnotationHubData/man/readMetadataFromCsv.Rd AnnotationHubData/man/updateResources.Rd AnnotationHubData/man/upload_to_S3.Rd
AnnotationHubData/tests
AnnotationHubData/tests/AnnotationHubData_unit_tests.R
AnnotationHubData/vignettes
AnnotationHubData/vignettes/IntroductionToAnnotationHubData.Rmd

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