AnnotationHub v2.4.2

by Martin Morgan

Client to access AnnotationHub resources

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

Functions in AnnotationHub

Name Description
upload_to_S3 Upload a file to Amazon S3
makeGencodeFasta Recipe to add Gencode FASTA resources to AnnotationHub
getAnnotationHubOption Get and set options for default AnnotationHub behavior.
serve Serve an AnnotationHub resource
getAllResourcePaths Get all paths to resources
getAllKeytypes Get all the names of metadata keys
getAllKeys Get all keys for a given keytype
ImportPreparer-class Class ImportPreparer and generic newResources
AnnotationHub-objects AnnotationHub objects and their related methods and functions
flog flog
updateAllResources Update resources in AnnotationHub
makeEnsemblFasta Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.
AnnotationHubServer-package Server component of AnnotationHub
query Query the AnnotationHub metadata
AnnotationHub-package Light-weight AnnotationHub 3.0 Client
AnnotationHubResource-objects AnnotationHubResource objects and their related methods and functions
AnnotationHubMetadata-class Class "AnnotationHubMetadata" and methods
updateResources updateResources
AnnotationHubRecipes-package Transform public data resources into Bioconductor Data Structures ~~ package title ~~
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Details

Type Package
biocViews Infrastructure, DataImport, GUI, ThirdPartyClient
License Artistic-2.0
Collate AnnotationHubOption.R AllGenerics.R Hub-class.R db-utils.R AnnotationHub-class.R AnnotationHubResource-class.R AnnotationHubBEDResource-class.R AnnotationHubProteomicsResource-class.R AnnotationHubEpigenomeResource-class.R utilities.R sql-utils.R hub-utils.R cache-utils.R zzz.R
VignetteBuilder knitr
NeedsCompilation yes
Packaged 2015-07-13 21:40:41 UTC; mcarlson

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