Man pages for CharlesJB/ENCODExplorer
A compilation of ENCODE metadata
| 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... |
