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AnnotationHubData (development version)

AnnotationHubData

This is the development version of AnnotationHubData; for the stable release version, see AnnotationHubData.

Transform public data resources into Bioconductor Data Structures

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DOI: 10.18129/B9.bioc.AnnotationHubData

Bioconductor version: Development (3.23)

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

Author: Martin Morgan [ctb], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Paul Shannon [ctb], Lori Shepherd [ctb], Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("AnnotationHubData")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("AnnotationHubData")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AnnotationHubData")

Introduction to AnnotationHubData HTML

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Software

Version 1.41.0

In Bioconductor since BioC 3.2 (R-3.2) (10 years)

License Artistic-2.0

Depends R (>= 3.2.2), methods, utils, S4Vectors(>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, AnnotationHub(>= 2.15.15)

Imports GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, Seqinfo, GenomeInfoDb(>= 1.45.5), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl

System Requirements

URL

See More

Suggests RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub

Linking To

Enhances

Depends On Me ExperimentHubData

Imports Me AHMassBank, AHEnsDbs, EuPathDB

Suggests Me HubPub, EPICv2manifest, GenomicState, TENET.AnnotationHub, humanHippocampus2024, smokingMouse

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package AnnotationHubData_1.41.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/AnnotationHubData

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AnnotationHubData

Bioc Package Browser https://code.bioconductor.org/browse/AnnotationHubData/

Package Short Url https://bioconductor.org/packages/AnnotationHubData/

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