ENCODExplorer

This package is for version 3.11 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: 3.11

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>

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

Installation

To install this package, start R (version "4.0") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ENCODExplorer")
ENCODExplorer HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, Infrastructure, Software
Version 2.14.0
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
See More
Suggests RUnit, BiocGenerics, knitr, curl, httr, shiny, shinythemes, DT
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me TSRchitect
Links To Me
Build Report Build Report

Package Archives

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

Source Package ENCODExplorer_2.14.0.tar.gz
Windows Binary ENCODExplorer_2.14.0.zip
macOS 10.13 (High Sierra) ENCODExplorer_2.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ENCODExplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ENCODExplorer
Bioc Package Browser https://code.bioconductor.org/browse/ENCODExplorer/
Package Short Url https://bioconductor.org/packages/ENCODExplorer/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive