DuplexDiscovereR-package	DuplexDiscovereR
.addDGidsForTmpDGs	dot-addDGidsForTmpDGs
.addGeneCounts	dot-addGeneCounts
.annotateCisTrans	dot-annotateCisTrans
.compute_clusters_comp	dot-compute_clusters_comp
.DGIdToDuplexId	dot-DGIdToDuplexId
.getStartEndOvl	dot-getStartEndOvl
.gv_plotboxes	dot-gv_plotboxes
.gv_updatepars	dot-gv_updatepars
annotateGI	annotateGI
availableDisplayPars	availableDisplayPars
calculateLigationPvalues	calculateLigationPvalues
classifyTwoArmChimeras	classifyTwoArmChimeras
clusterDuplexGroups	clusterDuplexGroups
collapseIdenticalReads	collapseIdenticalReads
collapseSimilarChimeras	collapseSimilarChimeras
collapse_duplex_groups	collapse_duplex_groups
col_check_rename	col_check_rename
compareMultipleInteractions	compareMultipleInteractions
computeGISelfOverlaps	computeGISelfOverlaps
convert_gi_to_ranges	convert_gi_to_ranges
dd_get_chimeric_reads	dd_get_chimeric_reads
dd_get_chimeric_reads,DuplexDiscovererResults-method	dd_get_chimeric_reads
dd_get_chimeric_reads_stats	dd_get_chimeric_reads_stats
dd_get_chimeric_reads_stats,DuplexDiscovererResults-method	dd_get_chimeric_reads_stats
dd_get_duplex_groups	dd_get_duplex_groups
dd_get_duplex_groups,DuplexDiscovererResults-method	dd_get_duplex_groups
dd_get_reads_classes	dd_get_reads_classes
dd_get_reads_classes,DuplexDiscovererResults-method	dd_get_reads_classes
dd_get_run_stats	dd_get_run_stats
dd_get_run_stats,DuplexDiscovererResults-method	dd_get_run_stats
drawGD,DuplexTrack-method	drawGD-DuplexTrack-method
DuplexDiscovereR	DuplexDiscovereR
DuplexDiscovererResults	DuplexDiscovererResults
DuplexDiscovererResults-class	DuplexDiscovererResults
DuplexTrack	DuplexTrack
getChimericJunctionTypes	getChimericJunctionTypes
getRNAHybrids	getRNAHybrids
getSpliceJunctionChimeras	getSpliceJunctionChimeras
get_arm_a	get_arm_a
get_arm_b	get_arm_b
get_char_count_cigar	get_char_count_cigar
get_chimeric_junctions_onestrand	get_chimeric_junctions_onestrand
get_colnames_and_types_for_input	get_colnames_and_types_for_input
makeDfFromGi	makeDfFromGi
makeGiFromDf	makeGiFromDf
preproc_chim_junction_out_pe	preproc_chim_junction_out_pe
preproc_chim_junction_out_se	preproc_chim_junction_out_se
preproc_generic	preproc_generic
preproc_generic_gi	preproc_generic_gi
refresh_gi	refresh_gi
RNADuplexesGeneCounts	RNADuplexesGeneCounts
RNADuplexesRawBed	RNADuplexesRawBed
RNADuplexesRawChimSTAR	RNADuplexesRawChimSTAR
RNADuplexSampleClustReads	RNADuplexSampleClustReads
RNADuplexSampleDGs	RNADuplexSampleDGs
RNADuplexSampleGI	RNADuplexSampleGI
runDuplexDiscoPreproc	runDuplexDiscoPreproc
runDuplexDiscoverer	runDuplexDiscoverer
SampleGeneAnnoGR	SampleGeneAnnoGR
SampleSmallGI	SampleSmallGI
SampleSpliceJncGR	SampleSpliceJncGR
show,DuplexDiscovererResults-method	show-DuplexDiscovererResults-method
show,DuplexTrack-method	show-DuplexTrack-method
subset_gi	subset_gi
writeGiToSAMfile	writeGiToSAMfile
