ENCODExplorer

DOI: 10.18129/B9.bioc.ENCODExplorer    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 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: 3.14

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 [aut, cre], Audrey Lemacon [aut], Eric Fournier [aut], Louis Gendron [ctb], Astrid-Louise Deschenes [ctb], Arnaud Droit [aut]

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

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

PDF		Reference Manual

Details

biocViews	DataImport, Infrastructure, Software
Version	2.20.0
In Bioconductor since	BioC 3.1 (R-3.2) (7 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
LinkingTo
Suggests	RUnit, BiocGenerics, knitr, curl, httr, shiny, shinythemes, DT
SystemRequirements
Enhances
URL
BugReports	https://github.com/CharlesJB/ENCODExplorer/issues
Depends On Me
Imports Me
Suggests Me	TSRchitect
Links To Me
Build Report

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