AnnotationHub: Client to access AnnotationHub resources
Version 2.8.1

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.

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AuthorMartin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]
Bioconductor views DataImport GUI Infrastructure ThirdPartyClient
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.8.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AnnotationHub")

Man pages

AnnotationHub-class: AnnotationHub objects and their related methods and functions
AnnotationHub-package: Light-weight AnnotationHub 3.0 Client
AnnotationHubResource-class: AnnotationHubResource objects and their related methods and...
getAnnotationHubOption: Get and set options for default AnnotationHub behavior.
listResources: Utility functions for discovering package-specific Hub...

Functions

$,Hub-method Man page
.Hub Man page
.db_close Man page
AnnotationHub Man page Source code
AnnotationHub-class Man page
AnnotationHub-package Man page
AnnotationHubResource-class Man page
DollarNames.Hub Source code
Hub Source code
Hub-class Man page
Hub_get1 Source code
[,Hub,character,missing-method Man page
[,Hub,logical,missing-method Man page
[,Hub,numeric,missing-method Man page
[<-,Hub,character,missing,Hub-method Man page
[<-,Hub,logical,missing,Hub-method Man page
[<-,Hub,numeric,missing,Hub-method Man page
[[,Hub,character,missing-method Man page
[[,Hub,numeric,missing-method Man page
as.list,Hub-method Man page
as.list.Hub Man page Source code
ask Source code
biocVersionDate Source code
c,Hub-method Man page
cache Man page
cache,AnnotationHub-method Man page
cache,Hub-method Man page
cache<- Man page
cache<-,Hub-method Man page
cache_internal Source code
cache_path Source code
class:AnnotationHub Man page
class:AnnotationHubResource Man page
class:Hub Man page
collapse_as_list Source code
collapse_as_string Source code
count_join_resources Source code
count_resources Source code
create_cache Source code
d_as_single_string Source code
dataclass Source code
datapathIds Source code
db_close Source code
db_create_index Source code
db_current Source code
db_get Source code
db_get_db Source code
db_index Source code
db_index_file Source code
db_index_load Source code
db_is_valid Source code
db_open Source code
db_query Source code
db_uid Source code
db_uid0 Source code
dbconn,Hub-method Man page
dbfile,Hub-method Man page
display Man page Source code
display,Hub-method Man page
fileName,Hub-method Man page
filterResources_AH Source code
getAnnotationHubOption Man page Source code
getHub Man page
getHub,AnnotationHubResource-method Man page
guessIsCircular Source code
gunzip Source code
httr_proxy Source code
hubCache Man page
hubCache,AnnotationHubResource-method Man page
hubCache,Hub-method Man page
hubDate Man page
hubDate,Hub-method Man page
hubUrl Man page
hubUrl,AnnotationHubResource-method Man page
hubUrl,Hub-method Man page
hub_cache_resource Source code
hub_data_path Source code
hub_metadata_path Source code
hub_option_key Source code
hub_resource Source code
hub_resource_path Source code
length,Hub-method Man page
listResources Man page
listResources,AnnotationHub-method Man page
loadResources Man page
loadResources,AnnotationHub-method Man page
makeGrFromCharacterString Source code
mapAbbr2FullName Source code
mcols,Hub-method Man page
metadataForAH Source code
named_cache_path Source code
names,Hub-method Man page
names_for_ids Source code
onLoad Source code
package Man page
package,Hub-method Man page
possibleDates Man page Source code Source code
pprintf0 Source code
pprintf1 Source code
query Man page
query,Hub-method Man page
query_as_data.frame Source code
rdataclass Source code
rdatapath Source code
recordStatus Man page
recordStatus,Hub-method Man page
removeCache Man page Source code
resource_column Source code
resource_columns Source code
resource_table Source code
restrictDateByVersion Source code
setAnnotationHubOption Man page Source code
show Source code
show,AnnotationHub-method Man page
show,AnnotationHubResource-method Man page
show,Hub-method Man page
show1 Source code
snapshotDate Man page
snapshotDate,Hub-method Man page
snapshotDate<- Man page
snapshotDate<-,Hub-method Man page
sourcelastmodifieddate Source code
sourcesize Source code
sourcetype Source code
sourceurl Source code
subset,Hub-method Man page
tags Source code
tidyGRanges Source code
title_data.frame Source code
uid0 Source code
utilities Man page
valid.Hub Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/AnnotationHub-class.R
R/AnnotationHubOption.R
R/AnnotationHubResource-class.R
R/BEDResource-class.R
R/EnsDbResource-class.R
R/EpigenomeResource-class.R
R/Hub-class.R
R/Hub-utils.R
R/ProteomicsResource-class.R
R/cache-utils.R
R/db-utils.R
R/sql-utils.R
R/utilities.R
R/zzz.R
build
build/vignette.rds
inst
inst/doc
inst/doc/AnnotationHub-HOWTO.R
inst/doc/AnnotationHub-HOWTO.Rmd
inst/doc/AnnotationHub-HOWTO.html
inst/doc/AnnotationHub.R
inst/doc/AnnotationHub.Rmd
inst/doc/AnnotationHub.html
inst/scripts
inst/scripts/shinyTest.R
inst/scripts/test.R
inst/unitTests
inst/unitTests/test_AnnotationHub-class.R
inst/unitTests/test_cache.R
inst/unitTests/test_tidyGRanges.R
inst/unitTests/test_utilities.R
man
man/AnnotationHub-class.Rd
man/AnnotationHub-package.Rd
man/AnnotationHubResource-class.Rd
man/getAnnotationHubOption.Rd
man/listResources.Rd
tests
tests/runTests.R
vignettes
vignettes/AnnotationHub-HOWTO.Rmd
vignettes/AnnotationHub.Rmd
vignettes/display.png
AnnotationHub documentation built on May 20, 2017, 10:31 p.m.