Package: AnnotationHub 3.15.0
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_3.15.0.tar.gz
AnnotationHub_3.15.0.zip(r-4.5)AnnotationHub_3.15.0.zip(r-4.4)AnnotationHub_3.15.0.zip(r-4.3)
AnnotationHub_3.15.0.tgz(r-4.4-any)AnnotationHub_3.15.0.tgz(r-4.3-any)
AnnotationHub_3.15.0.tar.gz(r-4.5-noble)AnnotationHub_3.15.0.tar.gz(r-4.4-noble)
AnnotationHub_3.15.0.tgz(r-4.4-emscripten)AnnotationHub_3.15.0.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')) |
Bug tracker:https://github.com/bioconductor/annotationhub/issues
On BioConductor:AnnotationHub-3.13.3(bioc 3.20)AnnotationHub-3.12.0(bioc 3.19)
infrastructuredataimportguithirdpartyclientcore-package
Last updated 23 days agofrom:7a750df1a9. Checks:OK: 1 NOTE: 3 ERROR: 3. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 30 2024 |
R-4.5-win | ERROR | Oct 30 2024 |
R-4.5-linux | NOTE | Oct 30 2024 |
R-4.4-win | ERROR | Oct 30 2024 |
R-4.4-mac | NOTE | Oct 30 2024 |
R-4.3-win | ERROR | Oct 30 2024 |
R-4.3-mac | NOTE | Oct 30 2024 |
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.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2023-12-11
Started: 2014-10-30
AnnotationHub How-To's
Rendered fromAnnotationHub-HOWTO.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2024-04-18
Started: 2015-05-20
Troubleshoot The Hubs
Rendered fromTroubleshootingTheHubs.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2023-12-11
Started: 2023-12-11
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 |