ENCODExplorer

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ENCODExplorer.

A compilation of ENCODE metadata


Bioconductor version: 3.13

This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.

Author: Charles Joly Beauparlant <charles.joly-beauparlant at crchul.ulaval.ca>, Audrey Lemacon <lemacon.audrey at ulaval.ca>, Eric Fournier <Fournier.Eric.2 at crchudequebec.ulaval.ca>, Louis Gendron <louisg.212 at gmail.com>, Astrid-Louise Deschenes <astrid-louise.deschenes at crchudequebec.ulaval.ca>, Arnaud Droit <arnaud.droit at crchudequebec.ulaval.ca>

Maintainer: Charles Joly Beauparlant <charles.joly-beauparlant at crchul.ulaval.ca>

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

Installation

To install this package, start R (version "4.1") and enter:


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

BiocManager::install("ENCODExplorer")

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

Documentation

Reference Manual PDF

Details

biocViews DataImport, Infrastructure, Software
Version 2.18.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends R (>= 3.6)
Imports methods, tools, jsonlite, RCurl, tidyr, data.table, dplyr, stringr, stringi, utils, AnnotationHub, GenomicRanges, rtracklayer, S4Vectors, GenomeInfoDb, ENCODExplorerData
System Requirements
URL
Bug Reports https://github.com/CharlesJB/ENCODExplorer/issues
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Suggests RUnit, BiocGenerics, knitr, curl, httr, shiny, shinythemes, DT
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Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/ENCODExplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ENCODExplorer
Package Short Url https://bioconductor.org/packages/ENCODExplorer/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive