.addDGidsForTmpDGs      Helper function to add ids to the duplex groups
                        missed during global clustering
.addGeneCounts          Helper function to add count data to metadata
                        of 'GInteractions'
annotateGI              Annotate RNA duplexes with features
availableDisplayPars    The default display parameters for a
                        'DuplexTrack' object
calculateLigationPvalues
                        Calculate ligation-based significance
                        statistics for RNA duplexes
classifyTwoArmChimeras
                        Wrapper for classification of the 2arm chimeric
                        reads
clusterDuplexGroups     Cluster RNA duplexes in 'GInteractions' object
collapse_duplex_groups
                        Collapse the reads into the duplex groups after
                        clustering
collapseIdenticalReads
                        Collapses identical interactions
collapseSimilarChimeras
                        Call clustering multiple times to collapse
                        similar reads into duplex groups
compareMultipleInteractions
                        Compare multiple RNA-RNA interactions sets
computeGISelfOverlaps   Find overlaps between entries in
                        'GInteractions'
convert_gi_to_ranges    Convert 'GInteractions' object to 'Granges'
dd_get_chimeric_reads   Accessor for 'chimeric_reads' Slot
dd_get_chimeric_reads_stats
                        Accessor for 'chimeric_reads_stats' Slot
dd_get_duplex_groups    Accessor for 'duplex_groups' slot
dd_get_reads_classes    Accessor for 'reads_classes' Slot
dd_get_run_stats        Accessor for 'run_stats' Slot
DuplexDiscovereR        Analysis of the data from RNA duplex probing
                        experiments
DuplexDiscovererResults-class
                        DuplexDiscovererResults
DuplexTrack             class for the visualization of RNA duplexes
get_char_count_cigar    Count the length of the key type in CIGAR
                        string
getChimericJunctionTypes
                        Classify chimeric junctions of two-arm reads
                        into types
getRNAHybrids           Run prediciton of RNA hybridization
getSpliceJunctionChimeras
                        Identify chimeric junctions coinciding with the
                        splice junctions
makeDfFromGi            Convert GInteractions to tibble
makeGiFromDf            Convert Dataframe to GInteractions
preproc_chim_junction_out_se
                        Processing of of the STAR SE
                        Chimeric.junction.out
RNADuplexesGeneCounts   Gene counts on human chromosome 22, embryonic
                        stem cells
RNADuplexesRawBed       Chimeric reads of SPLASH converted to .bedpe
                        fromat
RNADuplexesRawChimSTAR
                        Chimeric reads of SPLASH
RNADuplexSampleClustReads
                        RNA duplex reads of SPLASH, clustered and
                        assigned to duplex groups
RNADuplexSampleDGs      RNA duplex reads of SPLASH, clustered and
                        collapsed to duplex groups
RNADuplexSampleGI       RNA duplex reads of SPLASH derived from
                        chimeric alignments
runDuplexDiscoPreproc   Run pre-processing of chimeric reads input
runDuplexDiscoverer     Executes all steps of DuplexDiscovereR pipeline
SampleGeneAnnoGR        Gene coordinates on human chromosome 22
SampleSmallGI           RNA duplex reads of SPLASH derived from
                        chimeric alignments
SampleSpliceJncGR       Gene coordinates on human chromosome 22
show,DuplexDiscovererResults-method
                        Show Method for DuplexDiscovererResults class
show,DuplexTrack-method
                        Show method for DuplexTrack
trimAroundJunction      Extract regions around chimeric junction
writeGiToSAMfile        Write reads to sam file
