Package: AnnotationHub 3.13.0

Bioconductor Package Maintainer

AnnotationHub: 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.

Authors:Bioconductor Package Maintainer [cre], Martin Morgan [aut], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Valerie Oberchain [ctb], Kayla Morrell [ctb], Lori Shepherd [aut]

AnnotationHub_3.13.0.tar.gz
AnnotationHub_3.13.0.zip(r-4.5)AnnotationHub_3.13.0.zip(r-4.4)AnnotationHub_3.13.0.zip(r-4.3)
AnnotationHub_3.13.0.tgz(r-4.4-any)AnnotationHub_3.13.0.tgz(r-4.3-any)
AnnotationHub_3.13.0.tar.gz(r-4.5-noble)AnnotationHub_3.13.0.tar.gz(r-4.4-noble)
AnnotationHub_3.13.0.tgz(r-4.4-emscripten)AnnotationHub_3.13.0.tgz(r-4.3-emscripten)
AnnotationHub.pdf |AnnotationHub.html✨
AnnotationHub/json (API)
NEWS

# Install 'AnnotationHub' in R:
install.packages('AnnotationHub', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/annotationhub/issues

On BioConductor:AnnotationHub-3.13.0(bioc 3.20)AnnotationHub-3.12.0(bioc 3.19)

bioconductor-package

38 exports 6.32 score 58 dependencies 101 dependents 39 mentions

Last updated 2 months agofrom:cfa9c048ff

Exports:.db_close.DollarNames.Hub.httr_proxy.Hub.hub_option_keyAnnotationHubas.listas.list.Hubcachecache<-convertHubdbconndbfileDispatchClassListfileNamegetAnnotationHubOptiongetHubgetInfoOnIdshubCachehubDatehubUrlisLocalHubisLocalHub<-listResourcesloadResourcesmcolspackagepossibleDatesqueryrecordStatusrefreshHubremoveCacheremoveResourcessetAnnotationHubOptionshowsnapshotDatesnapshotDate<-subset

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6rappdirsrlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc

AnnotationHub: Access the AnnotationHub Web Service

Rendered fromAnnotationHub.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-12-11
Started: 2014-10-30

AnnotationHub How-To's

Rendered fromAnnotationHub-HOWTO.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-04-18
Started: 2015-05-20

Troubleshoot The Hubs

Lori Shepherd

Rendered fromTroubleshootingTheHubs.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-12-11
Started: 2023-12-11

Readme and manuals

Help Manual

Help pageTopics
Light-weight AnnotationHub 3.0 ClientAnnotationHub-package
AnnotationHub objects and their related methods and functions$,Hub-method .db_close .Hub AnnotationHub AnnotationHub-class as.list,Hub-method as.list.Hub c,Hub-method cache cache,AnnotationHub-method cache,Hub-method cache<- cache<-,Hub-method class:AnnotationHub class:Hub dbconn,Hub-method dbfile,Hub-method fileName,Hub-method Hub-class hubCache hubCache,Hub-method hubDate hubDate,Hub-method hubUrl hubUrl,Hub-method isLocalHub isLocalHub,Hub-method isLocalHub<- isLocalHub<-,Hub-method length,Hub-method mcols,Hub-method names,Hub-method package package,Hub-method possibleDates query query,Hub-method recordStatus recordStatus,Hub-method refreshHub removeCache removeResources removeResources,character-method removeResources,missing-method show,AnnotationHubResource-method show,Hub-method snapshotDate snapshotDate,Hub-method snapshotDate<- snapshotDate<-,Hub-method subset,Hub-method [,Hub,character,missing-method [,Hub,logical,missing-method [,Hub,numeric,missing-method [<-,Hub,character,missing,Hub-method [<-,Hub,logical,missing,Hub-method [<-,Hub,numeric,missing,Hub-method [[,Hub,character,missing-method [[,Hub,numeric,missing-method
Convert old Hub to new Hub structureconvertHub
Get and set options for default AnnotationHub behavior.getAnnotationHubOption setAnnotationHubOption
Get information for selected idsgetInfoOnIds getInfoOnIds,character-method getInfoOnIds,missing-method getInfoOnIds,numeric-method Hub-utils
Utility functions for discovering package-specific Hub resources.listResources loadResources utilities
Utility function to list currently available dispatchClass.DispatchClassList utils