Analysis of the data from RNA duplex probing experiments

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Documentation for package ‘DuplexDiscovereR’ version 1.3.2

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

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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