AnnotationHubData: Transform public data resources into Bioconductor Data Structures

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These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

Author
Martin Morgan [ctb], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Paul Shannon [ctb], Bioconductor Package Maintainer [cre]
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.4.0

View on Bioconductor

Man pages

AnnotationHubData-package
Transform public data resources into Bioconductor Data...
AnnotationHubMetadata-class
Class '"AnnotationHubMetadata"' and methods
flog
flog
ImportPreparer-class
Class 'ImportPreparer' and generic 'newResources'
makeAnnotationHubMetadata
Make AnnotationHubMetadata objects from csv file of metadata
makeEnsemblFasta
Functions to convert Ensembl FASTA files to FaFile and...
makeGencodeFasta
Recipe to add Gencode FASTA resources to AnnotationHub
readMetadataFromCsv
Reads a csv file of resource metadata into a data.frame
updateResources
updateResources
upload_to_S3
Upload a file to Amazon S3

Files in this package

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