Man pages for CharlesJB/ENCODExplorer
A compilation of ENCODE metadata

buildConsensusPeaksCalculates the consensus peaks defined by the results of a...
buildExpressionSummaryCalculates average expression levels of the results of a...
choose_interactive_valueInteractively select one of many possible metadata values.
clean_columnClean a single column of the data.frame
clean_tableClean a data.frame that was produced by ENCODE REST API
combined_regions-GenomicOverlaps-methodReturns the combined regions from a GenomicOverlaps object.
combined_regions-set-GenomicOverlaps-GRanges-methodSet the combined regions from a GenomicOverlaps object.
consensus_indicesDetermines which regions form a "consensus" from all input...
consensus_regionsDetermines which regions form a "consensus" from all input...
createDesignCreate a design for the files associated with the result of a...
download_dt_fileDownloads all files inside a data.table.
downloadEncodedownloadEncode is used to download a serie of files or...
download_single_filedownload_single_file Downloads a single file and checks if...
ENCODEBindingConsensus-classENCODEBindingConsensus: consensus peaks derived from ENCODE...
ENCODEExpressionSummary-classENCODEExpressionSummary summarize means of expression across...
ENCODESummary-classENCODESummary objects: summaries of multiple ENCODE files.
ENCODExplorerENCODExplorer
fuzzySearchFuzzysearch is a searching function for a string or a list of...
GenomicOverlapsCreate a GenomicOverlaps object.
GenomicOverlaps-classGenomicOverlaps objects represent the overlaps of multiple...
get_encode_dfReturns a "light" version of ENCODE file metadata.
get_encode_df_demoGet a demo encode_df
get_encode_df_fullConcatenates all available file metadata into a single data...
initial_regions-GenomicOverlaps-methodReturns the initial regions from a GenomicOverlaps object.
intersect_indicesCalculate the intersection of a set of elements within a...
intersect_matrixReturns the intersection matrix from a GenomicOverlaps...
intersect_regionsCalculate the intersection of a set of elements within a...
length-GenomicOverlaps-methodReturns the number of elements of a GenomicOverlaps object.
names-GenomicOverlaps-methodReturns the names of the elements of a GenomicOverlaps...
names-set-GenomicOverlaps-character-methodSet names of the elements of a GenomicOverlaps object.
pairwise_overlapCalculate the pairwise overlaps of all factors within a...
queryConsensusPeaksQueries ENCODE for consensus peaks.
queryEncodeProduce a subset of data following predefined criteria
queryEncodeGenericProduce a subset of data following predefined criteria.
queryExpressionGenericQueries and returns average expression levels for a given...
queryGeneExpressionQueries and returns average gene expression level for a given...
queryTranscriptExpressionQueries and returns average transcript expression level for a...
searchEncodeSimulate a query on ENCODE website and return the result as a...
searchToqueryConvert searchEncode output in queryEncode output.
shinyEncodeLaunch a shiny interface for ENCODExplorer
split_by_metadataGiven a metadata data-frame and a vector of column names...
union_indicesCalculate the union of a set of elements within a...
union_regionsCalculate the union of a set of elements within a...
CharlesJB/ENCODExplorer documentation built on Oct. 12, 2019, 9:36 p.m.