Package: AnnotationHub 4.3.2

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_4.3.2.tar.gz
AnnotationHub_4.3.2.zip(r-4.7)AnnotationHub_4.3.2.zip(r-4.6)AnnotationHub_4.3.2.zip(r-4.5)
AnnotationHub_4.3.2.tgz(r-4.6-any)AnnotationHub_4.3.2.tgz(r-4.5-any)
AnnotationHub_4.3.2.tar.gz(r-4.7-any)AnnotationHub_4.3.2.tar.gz(r-4.6-any)
AnnotationHub_4.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
AnnotationHub/json (API)

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

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

On BioConductor:AnnotationHub-4.3.1(bioc 3.24)AnnotationHub-4.2.1(bioc 3.23)

infrastructuredataimportguithirdpartyclientcore-packageu24ca289073

12.87 score 19 stars 119 packages 4.6k scripts 39 mentions 38 exports 55 dependencies

Last updated from:b406e89030. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING225
linux-devel-x86_64NOTE366
source / vignettesOK345
linux-release-x86_64NOTE382
macos-release-arm64NOTE264
macos-oldrel-arm64NOTE251
windows-develNOTE277
windows-releaseNOTE265
windows-oldrelNOTE360
wasm-releaseOK220

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

Dependencies:AnnotationDbiaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml

AnnotationHub How-To's
Accessing Genome-Scale Data | Non-model organism gene annotations | Roadmap Epigenomics Project | Ensembl GTF and FASTA files for TxDb gene models and sequence queries | liftOver to map between genome builds | sessionInfo

Last update: 2026-06-15
Started: 2015-05-20

AnnotationHub: Access the AnnotationHub Web Service
AnnotationHub objects | Interactive retrieval of resources with BiocHubsShiny | Using AnnotationHub to retrieve data | Configuring AnnotationHub objects | AnnotationHub objects in a cluster environment | Creating an AnnotationHub Package or Converting to an AnnotationHub Package | Troubleshooting | Accessing Behind A Proxy | Other configuration options for resource downloading | Session info

Last update: 2025-05-15
Started: 2014-10-30

Troubleshoot The Hubs
Overview | Troubleshooting | Accessing Behind A Proxy | Other configuration options for resource downloading | Invalid Cache | Corrupt Cache | sqlite file | redownload of sqlite file | index file | resource path | resource id | Corrupt Database | Cannot retrieve resource | Offline localHub usage | Group Hub/Cache Access | Lock file Troubleshooting | Permissions | Cannot lock file / no lock available | Default Caching Location Update | Option 1: Move cache and files to new location | Option 2: Create a system environment variable | Option 3: Delete the old cache

Last update: 2025-05-15
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