AnnotationHubData v1.2.2

by Bioconductor Package Maintainer

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

imports	AnnotationDbi , AnnotationForge , Biobase , BiocGenerics , BiocInstaller , Biostrings , curl , DBI , futile , futile.logger (>= 1.3.0) , GenomeInfoDb , GenomicFeatures , GEOquery , httr , jsonlite , OrganismDbi , rBiopaxParser , Rsamtools , RSQLite , rtracklayer , XML , xml2
depends	AnnotationHub , base (>= 3.2.2) , GenomicRanges , IRanges (>= 2.3.23) , methods , R (>= 3.2.2) , S4Vectors (>= 0.7.21)
suggests	BiocStyle , grasp2db , knitr , RMySQL , RUnit
Contributors	Dan Tenenbaum, Bioconductor Package Maintainer, Marc Carlson, Sonali Arora, Martin Morgan, Paul Shannon

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