A compilation of ENCODE metadata

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Documentation for package ‘ENCODExplorer’ version 2.12.1

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ENCODExplorer-package ENCODExplorer
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.
clean_column Clean a single column of the data.frame
clean_table Clean a data.frame that was produced by ENCODE REST API
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.