# Analysis of the data from RNA duplex probing experiments

## Documentation for package ‘DuplexDiscovereR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

DuplexDiscovereR-package | Analysis of the data from RNA duplex probing experiments
.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 p-values and abundance fractions for RNA duplexes
classifyTwoArmChimeras | Wrapper for classification of the 2arm chimeric reads
clusterDuplexGroups | Cluster RNA duplexes in 'GInteractions' object
collapseIdenticalReads | Collapses identical interactions
collapseSimilarChimeras | Call clustering multiple times to collapse similar reads into duplex groups
collapse_duplex_groups | Collapse the reads into the duplex groups after clustering
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-method | Accessor for 'chimeric_reads' Slot
dd_get_chimeric_reads_stats | Accessor for 'chimeric_reads_stats' Slot
dd_get_chimeric_reads_stats-method | Accessor for 'chimeric_reads_stats' Slot
dd_get_duplex_groups | Accessor for 'duplex_groups' slot
dd_get_duplex_groups-method | Accessor for 'duplex_groups' slot
dd_get_reads_classes | Accessor for 'reads_classes' Slot
dd_get_reads_classes-method | Accessor for 'reads_classes' Slot
dd_get_run_stats | Accessor for 'run_stats' Slot
dd_get_run_stats-method | Accessor for 'run_stats' Slot
DuplexDiscovereR | Analysis of the data from RNA duplex probing experiments
DuplexDiscovererResults | DuplexDiscovererResults
DuplexDiscovererResults-class | DuplexDiscovererResults
DuplexTrack | class for the visualization of RNA duplexes
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
get_char_count_cigar | Count the length of the key type in CIGAR string
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-method | Show Method for DuplexDiscovererResults class
show-method | Show method for DuplexTrack
trimAroundJunction | Extract regions around chimeric junction
writeGiToSAMfile | Write reads to sam file