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.

AuthorMartin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.6.4

View on Bioconductor

Functions

AnnotationHub Man page
AnnotationHub-class Man page
AnnotationHub-package Man page
AnnotationHubResource-class Man page
as.list.Hub Man page
as.list,Hub-method Man page
cache Man page
cache<- Man page
cache,AnnotationHub-method Man page
cache<-,Hub-method Man page
cache,Hub-method Man page
c,Hub-method Man page
class:AnnotationHub Man page
class:AnnotationHubResource Man page
class:Hub Man page
.db_close Man page
dbconn,Hub-method Man page
dbfile,Hub-method Man page
display Man page
display,Hub-method Man page
fileName,Hub-method Man page
getAnnotationHubOption Man page
getHub Man page
getHub,AnnotationHubResource-method Man page
.Hub Man page
hubCache Man page
hubCache,AnnotationHubResource-method Man page
hubCache,Hub-method Man page
[<-,Hub,character,missing,Hub-method Man page
[,Hub,character,missing-method Man page
[[,Hub,character,missing-method Man page
Hub-class Man page
hubDate Man page
hubDate,Hub-method Man page
[<-,Hub,logical,missing,Hub-method Man page
[,Hub,logical,missing-method Man page
$,Hub-method Man page
[<-,Hub,numeric,missing,Hub-method Man page
[,Hub,numeric,missing-method Man page
[[,Hub,numeric,missing-method Man page
hubUrl Man page
hubUrl,AnnotationHubResource-method Man page
hubUrl,Hub-method Man page
length,Hub-method Man page
listResources Man page
listResources,AnnotationHub-method Man page
loadResources Man page
loadResources,AnnotationHub-method Man page
mcols,Hub-method Man page
names,Hub-method Man page
package Man page
package,Hub-method Man page
possibleDates Man page
query Man page
query,Hub-method Man page
recordStatus Man page
recordStatus,Hub-method Man page
removeCache Man page
setAnnotationHubOption Man page
show,AnnotationHub-method Man page
show,AnnotationHubResource-method Man page
show,Hub-method Man page
snapshotDate Man page
snapshotDate<- Man page
snapshotDate<-,Hub-method Man page
snapshotDate,Hub-method Man page
subset,Hub-method Man page
utilities Man page

Files

AnnotationHub/DESCRIPTION
AnnotationHub/NAMESPACE
AnnotationHub/NEWS
AnnotationHub/R
AnnotationHub/R/AllGenerics.R AnnotationHub/R/AnnotationHub-class.R AnnotationHub/R/AnnotationHubOption.R AnnotationHub/R/AnnotationHubResource-class.R AnnotationHub/R/BEDResource-class.R AnnotationHub/R/EpigenomeResource-class.R AnnotationHub/R/GenomicScoresResource-class.R AnnotationHub/R/Hub-class.R AnnotationHub/R/Hub-utils.R AnnotationHub/R/ProteomicsResource-class.R AnnotationHub/R/cache-utils.R AnnotationHub/R/db-utils.R AnnotationHub/R/sql-utils.R AnnotationHub/R/utilities.R AnnotationHub/R/zzz.R
AnnotationHub/build
AnnotationHub/build/vignette.rds
AnnotationHub/inst
AnnotationHub/inst/doc
AnnotationHub/inst/doc/AnnotationHub-HOWTO.R
AnnotationHub/inst/doc/AnnotationHub-HOWTO.Rmd
AnnotationHub/inst/doc/AnnotationHub-HOWTO.html
AnnotationHub/inst/doc/AnnotationHub.R
AnnotationHub/inst/doc/AnnotationHub.Rmd
AnnotationHub/inst/doc/AnnotationHub.html
AnnotationHub/inst/scripts
AnnotationHub/inst/scripts/shinyTest.R
AnnotationHub/inst/scripts/test.R
AnnotationHub/inst/unitTests
AnnotationHub/inst/unitTests/test_AnnotationHub-class.R
AnnotationHub/inst/unitTests/test_cache.R
AnnotationHub/inst/unitTests/test_tidyGRanges.R
AnnotationHub/inst/unitTests/test_utilities.R
AnnotationHub/man
AnnotationHub/man/AnnotationHub-class.Rd AnnotationHub/man/AnnotationHub-package.Rd AnnotationHub/man/AnnotationHubResource-class.Rd AnnotationHub/man/getAnnotationHubOption.Rd AnnotationHub/man/listResources.Rd
AnnotationHub/tests
AnnotationHub/tests/runTests.R
AnnotationHub/vignettes
AnnotationHub/vignettes/AnnotationHub-HOWTO.Rmd
AnnotationHub/vignettes/AnnotationHub.Rmd
AnnotationHub/vignettes/display.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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