# A compilation of ENCODE metadata

## Documentation for package ‘ENCODExplorer’ version 2.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ENCODExplorer-package | ENCODExplorer
clean_column | Clean a single column of the data.frame
clean_table | Clean a data.frame that was produced by extract_table
createDesign | Create a design for the files associated with the result of a queryEncode, fuzzySearch research or a 'data.table' from createDesign.
downloadEncode | downloadEncode is used to download a serie of files or datasets using their accession.
download_dt_file | Downloads all files inside a data.table.
download_single_file | download_single_file Downloads a single file and checks if md5 checksums match.
ENCODExplorer | ENCODExplorer
encode_df | Metadata from the ENCODE database in a R object. The tables were generated with the 'prepare_ENCODEdb' function.
export_ENCODEdb_matrix | Extract essential informations from a list of data.table in a 'list' of 'data.table's
extract_table | Extract a data.frame corresponding to a table in ENCODE database
fuzzySearch | Fuzzysearch is a searching function for a string or a list of string within the encode_df 'data.table'. For faster processing, pass encode_df object as database parameter.
get_encode_types | A list of known tables from ENCODE database.
get_schemas | Extract the schemas from ENCODE's github
prepare_ENCODEdb | Create the list of data.table for the tables in ENCODE
queryEncode | Produce a subset of data following predefined criteria
searchEncode | Simulate a query on ENCODE website and return the result as a 'data.frame'
searchToquery | Convert searchEncode output in queryEncode output.
shinyEncode | Launch a shiny interface for ENCODExplorer