AnnotationHubData

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see AnnotationHubData.

Transform public data resources into Bioconductor Data Structures

Bioconductor version: 3.6

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], 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 "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Software

Version 1.8.1

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(>= 2.9.14)

Imports GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocInstaller, biocViews, AnnotationDbi, Biobase, Biostrings, DBI, GEOquery, GenomeInfoDb, OrganismDbi, RSQLite, rBiopaxParser, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl

System Requirements

URL

Suggests RUnit, knitr, BiocStyle, grasp2db, BiocInstaller

Linking To

Enhances

Depends On Me ExperimentHubData, ProteomicsAnnotationHubData

Imports Me AHEnsDbs

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package AnnotationHubData_1.8.1.tar.gz

Windows Binary AnnotationHubData_1.8.1.zip

Mac OS X 10.11 (El Capitan) AnnotationHubData_1.8.1.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

Old Source Packages for BioC 3.6 Source Archive