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ENCODExplorer: A compilation of ENCODE metadata

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.

Bioconductor Package

ENCODExplorer is now an official package of Bioconductor. The current release can be directly downloaded from their website: Current release

Authors

Charles Joly Beauparlant, Audrey Lemaçon and Arnaud Droit.

See Arnaud Droit Lab website.

Maintainer

Charles Joly Beauparlant

License

This package and the underlying ENCODExplorer code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

For more information on Artistic 2.0 License see http://opensource.org/licenses/Artistic-2.0

Bugs/Feature requests

If you have any bugs or feature requests, let us know. Thanks!

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Version

Version

1.4.3

License

Artistic-2.0

Maintainer

Charles Joly Beauparlant

Last Published

February 15th, 2017

Functions in ENCODExplorer (1.4.3)

clean_table

Clean a data.frame that was produced by extract_table
accession_df

Metadata from the ENCODE database in a R object. The tables were generated with the prepare_ENCODEdb function.
export_ENCODEdb_accession

Extract accession numbers from all the datasets of RSQLite databse in a data.frame
downloadEncode

Download files from the Internet.
export_ENCODEdb_matrix

Extract essential informations from the RSQLite databse in a list of data.frames
ENCODExplorer

ENCODExplorer
extract_table

Extract a data.frame corresponding to a table in ENCODE database
get_encode_types

A list of known tables from ENCODE database.
get_schemas

Extract the schemas from ENCODE's github
encode_df

Metadata from the ENCODE database in a R object. The tables were generated with the prepare_ENCODEdb function.
searchToquery

Convert searchEncode output in queryEncode output.
prepare_ENCODEdb

Create the RSQLite databse for the tables in ENCODE
update_ENCODExplorer

Create or update all the needed data for ENCODExplorer
resolveEncodeAccession

Return a data.frame containing basic datasets information from an accession number
queryEncode

Produce a subset of data following predefined criteria
searchEncode

Simulate a query on ENCODE website and return the result as a data.frame