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AnnotationHubData

Transform public data resources into Bioconductor Data Structures


Bioconductor version: Release (3.19)

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 "4.4") and enter:


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

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

Details

biocViews DataImport, Software
Version 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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, GenomeInfoDb(>= 1.15.4), 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, homosapienDEE2CellScore, smokingMouse
Links To Me
Build Report Build Report

Package Archives

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

Source Package AnnotationHubData_1.34.0.tar.gz
Windows Binary AnnotationHubData_1.34.0.zip
macOS Binary (x86_64) AnnotationHubData_1.34.0.tgz
macOS Binary (arm64) AnnotationHubData_1.34.0.tgz
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/
Package Downloads Report Download Stats