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AnnotationHub (version 2.4.2)

Client to access AnnotationHub resources

Description

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.

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Version

Version

2.4.2

License

Artistic-2.0

Maintainer

Martin Morgan

Last Published

February 15th, 2017

Functions in AnnotationHub (2.4.2)

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 ~~