# A compilation of ENCODE metadata

## Documentation for package ‘ENCODExplorer’ version 2.13.1

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

## Help Pages

buildConsensusPeaks | Calculates the consensus peaks defined by the results of a previously completed ENCODE query.
buildExpressionSummary | Calculates average expression levels of the results of a previously completed ENCODE query.
consensus | ENCODEBindingConsensus: consensus peaks derived from ENCODE files.
consensus-method | ENCODEBindingConsensus: consensus peaks derived from ENCODE files.
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.
ENCODEBindingConsensus-class | ENCODEBindingConsensus: consensus peaks derived from ENCODE files.
ENCODEExpressionSummary-class | ENCODEExpressionSummary summarize means of expression across ENCODE files.
ENCODESummary-class | ENCODESummary objects: summaries of multiple ENCODE files.
ENCODExplorer | ENCODExplorer
files | ENCODESummary objects: summaries of multiple ENCODE files.
files-method | ENCODESummary objects: summaries of multiple ENCODE files.
file_metadata | ENCODESummary objects: summaries of multiple ENCODE files.
file_metadata-method | ENCODESummary objects: summaries of multiple ENCODE files.
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_df | Returns a "light" version of ENCODE file metadata.
get_encode_df_demo | Get a demo encode_df
get_encode_df_full | Concatenates all available file metadata into a single data table.
length-method | ENCODESummary objects: summaries of multiple ENCODE files.
metadata-method | ENCODESummary objects: summaries of multiple ENCODE files.
metric | ENCODEExpressionSummary summarize means of expression across ENCODE files.
metric-method | ENCODEExpressionSummary summarize means of expression across ENCODE files.
metric_data | ENCODEExpressionSummary summarize means of expression across ENCODE files.
metric_data-method | ENCODEExpressionSummary summarize means of expression across ENCODE files.
names-method | ENCODESummary objects: summaries of multiple ENCODE files.
names<--method | ENCODEBindingConsensus: consensus peaks derived from ENCODE files.
names<--method | ENCODEExpressionSummary summarize means of expression across ENCODE files.
names<--method | ENCODESummary objects: summaries of multiple ENCODE files.
peaks | ENCODEBindingConsensus: consensus peaks derived from ENCODE files.
peaks-method | ENCODEBindingConsensus: consensus peaks derived from ENCODE files.
queryConsensusPeaks | Queries ENCODE for consensus peaks.
queryEncode | Produce a subset of data following predefined criteria
queryEncodeGeneric | Produce a subset of data following predefined criteria.
queryExpressionGeneric | Queries and returns average expression levels for a given biosample_name.
queryGeneExpression | Queries and returns average gene expression level for a given biosample_name.
queryTranscriptExpression | Queries and returns average transcript expression level for a given biosample_name.
raw_data | ENCODEExpressionSummary summarize means of expression across ENCODE files.
raw_data-method | ENCODEExpressionSummary summarize means of expression across ENCODE files.
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
show-method | ENCODEBindingConsensus: consensus peaks derived from ENCODE files.
show-method | ENCODEExpressionSummary summarize means of expression across ENCODE files.
show-method | ENCODESummary objects: summaries of multiple ENCODE files.