Package: AnnotationHub 4.3.0

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_4.3.0.tar.gz
AnnotationHub_4.3.0.zip(r-4.7)AnnotationHub_4.3.0.zip(r-4.6)AnnotationHub_4.3.0.zip(r-4.5)
AnnotationHub_4.3.0.tgz(r-4.6-any)AnnotationHub_4.3.0.tgz(r-4.5-any)
AnnotationHub_4.3.0.tar.gz(r-4.7-any)AnnotationHub_4.3.0.tar.gz(r-4.6-any)
AnnotationHub_4.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
AnnotationHub/json (API)
NEWS

# 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-4.3.0(bioc 3.24)AnnotationHub-4.2.0(bioc 3.23)

infrastructuredataimportguithirdpartyclientcore-packageu24ca289073

12.49 score 19 stars 115 packages 3.6k scripts 20k downloads 39 mentions 38 exports 55 dependencies

Last updated from:1e2b7d074a. Checks:5 WARNING, 3 ERROR, 1 FAIL, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING218
linux-devel-x86_64WARNING420
source / vignettesERROR369
linux-release-x86_64WARNING372
macos-release-arm64WARNING232
macos-oldrel-arm64WARNING254
windows-develERROR269
windows-releaseERROR253
windows-oldrelFAIL16
wasm-releaseOK188

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

Dependencies:AnnotationDbiaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml

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