AnnotationHubData v1.2.2

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.

Functions in AnnotationHubData

Name Description
AnnotationHubRecipes-package Transform public data resources into Bioconductor Data Structures ~~ package title ~~
flog flog
makeEnsemblFasta Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.
ImportPreparer-class Class ImportPreparer and generic newResources
updateResources updateResources
AnnotationHubMetadata-class Class "AnnotationHubMetadata" and methods
makeGencodeFasta Recipe to add Gencode FASTA resources to AnnotationHub
upload_to_S3 Upload a file to Amazon S3
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Details

Type Package
License Artistic-2.0
LazyLoad yes
biocViews DataImport
VignetteBuilder knitr
Collate Message-class.R ImportPreparer-class.R makeAnnotationHubResource.R HubMetadata-class.R AnnotationHubMetadata-class.R utils.R updateResources.R ahmToJson.R webAccessFunctions.R makeBioPaxImporter.R makeChEA.R makedbSNPVCF.R makeEncodeDCC.R makeEnsemblGtfToGRanges.R makeEnsemblFasta.R makeEpigenomeRoadmap.R makeGencodeFasta.R makeGenecodeGFF.R makeGrasp2Db.R makeGSE62944ToExpressionSet.R makeHaemCode.R makeInparanoid8ToDbs.R makeNCBIToOrgDbs.R makeRecentOrgPkgsToDbs.R makePazar.R makeRefNet.R makeUCSCChain.R makeUCSC2Bit.R makeUCSCTracks.R trackWithAuxiliaryTableToGRangesRecipe.R UCSCTrackUpdateChecker.R makeEnsemblTwoBit.R

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