buildConsensusPeaks | Calculates the consensus peaks defined by the results of a... |
buildExpressionSummary | Calculates average expression levels of the results of a... |
choose_interactive_value | Interactively select one of many possible metadata values. |
combined_regions-GenomicOverlaps-method | Returns the combined regions from a GenomicOverlaps object. |
combined_regions-set-GenomicOverlaps-GRanges-method | Set the combined regions from a GenomicOverlaps object. |
consensus_indices | Determines which regions form a "consensus" from all input... |
consensus_regions | Determines which regions form a "consensus" from all input... |
createDesign | Create a design for the files associated with the result of a... |
download_dt_file | Downloads all files inside a data.table. |
downloadEncode | downloadEncode is used to download a serie of files or... |
download_single_file | download_single_file Downloads a single file and checks if... |
ENCODEBindingConsensus-class | ENCODEBindingConsensus: consensus peaks derived from ENCODE... |
ENCODEExpressionSummary-class | ENCODEExpressionSummary summarize means of expression across... |
ENCODESummary-class | ENCODESummary objects: summaries of multiple ENCODE files. |
ENCODExplorer | ENCODExplorer |
fuzzySearch | Fuzzysearch is a searching function for a string or a list of... |
GenomicOverlaps | Create a GenomicOverlaps object. |
GenomicOverlaps-class | GenomicOverlaps objects represent the overlaps of multiple... |
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... |
initial_regions-GenomicOverlaps-method | Returns the initial regions from a GenomicOverlaps object. |
intersect_indices | Calculate the intersection of a set of elements within a... |
intersect_matrix | Returns the intersection matrix from a GenomicOverlaps... |
intersect_regions | Calculate the intersection of a set of elements within a... |
length-GenomicOverlaps-method | Returns the number of elements of a GenomicOverlaps object. |
names-GenomicOverlaps-method | Returns the names of the elements of a GenomicOverlaps... |
names-set-GenomicOverlaps-character-method | Set names of the elements of a GenomicOverlaps object. |
pairwise_overlap | Calculate the pairwise overlaps of all factors within a... |
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... |
queryGeneExpression | Queries and returns average gene expression level for a given... |
queryTranscriptExpression | Queries and returns average transcript expression level for a... |
searchEncode | Simulate a query on ENCODE website and return the result as a... |
searchToquery | Convert searchEncode output in queryEncode output. |
shinyEncode | Launch a shiny interface for ENCODExplorer |
split_by_metadata | Given a metadata data-frame and a vector of column names... |
union_indices | Calculate the union of a set of elements within a... |
union_regions | Calculate the union of a set of elements within a... |
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