Package: AnnotationHub 4.3.0
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:
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
Last updated from:1e2b7d074a. Checks:5 WARNING, 3 ERROR, 1 FAIL, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
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| bioc-checks | WARNING | 218 | ||
| linux-devel-x86_64 | WARNING | 420 | ||
| source / vignettes | ERROR | 369 | ||
| linux-release-x86_64 | WARNING | 372 | ||
| macos-release-arm64 | WARNING | 232 | ||
| macos-oldrel-arm64 | WARNING | 254 | ||
| windows-devel | ERROR | 269 | ||
| windows-release | ERROR | 253 | ||
| windows-oldrel | FAIL | 16 | ||
| wasm-release | OK | 188 |
Exports:.db_close.DollarNames.Hub.getProxyValue.Hub.hub_option_keyAnnotationHubas.listas.list.Hubcachecache<-convertHubdbconndbfileDispatchClassListfileNamegetAnnotationHubOptiongetHubgetInfoOnIdshubCachehubDatehubUrlisLocalHubisLocalHub<-listResourcesloadResourcesmcolspackagepossibleDatesqueryrecordStatusrefreshHubremoveCacheremoveResourcessetAnnotationHubOptionshowsnapshotDatesnapshotDate<-subset
Dependencies:AnnotationDbiaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Light-weight AnnotationHub 3.0 Client | AnnotationHub-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 structure | convertHub |
| Get and set options for default AnnotationHub behavior. | getAnnotationHubOption setAnnotationHubOption |
| Get information for selected ids | getInfoOnIds 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 |
