AnnotationHubData

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Transform public data resources into Bioconductor Data Structures

Bioconductor version: Development (3.24)

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")):

Martin Morgan, Marc Carlson, Dan Tenenbaum, Sonali Arora, Paul Shannon, Lori Shepherd, Bioconductor Package Maintainer. AnnotationHubData: Transform public data resources into Bioconductor Data Structures. doi:10.18129/B9.bioc.AnnotationHubData, R package version 1.43.0, https://bioconductor.org/packages/AnnotationHubData.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
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	1.43.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 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

Suggests	RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub
Linking To
Enhances
Depends On Me	ExperimentHubData
Imports Me	AHEnsDbs, AHMassBank, EuPathDB
Suggests Me	EPICv2manifest, GenomicState, HubPub, humanHippocampus2024, smokingMouse, TENET.AnnotationHub
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	AnnotationHubData_1.43.0.tar.gz
Windows Binary (x86_64)	AnnotationHubData_1.43.0.zip
macOS Binary (big-sur-x86_64)	AnnotationHubData_1.43.0.tgz
macOS Binary (sonoma-arm64)	AnnotationHubData_1.43.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AnnotationHubData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AnnotationHubData
Package Short Url	https://bioconductor.org/packages/AnnotationHubData/
Package Downloads Report	Download Stats