amplican-package	amplican
$,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
AlignmentsExperimentSet	AlignmentsExperimentSet-class
AlignmentsExperimentSet-class	AlignmentsExperimentSet-class
alphabetQuality	alphabetQuality
amplican	amplican
amplicanAlign	amplicanAlign
amplicanConsensus	amplicanConsensus
amplicanFilter	amplicanFilter
amplicanMap	amplicanMap
amplicanNormalize	amplicanNormalize
amplicanOverlap	amplicanOverlap
amplicanPipeline	amplicanPipeline
amplicanPipelineConservative	amplicanPipelineConservative
amplicanReport	amplicanReport
amplicanSummarize	amplicanSummarize
amplican_print_reads	amplican_print_reads
as.list.AlignmentsExperimentSet	AlignmentsExperimentSet-class
assignedCount	assignedCount
assignedCount,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
barcodeData	barcodeData
barcodeData,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
barcodeData<-	barcodeData-set
barcodeData<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
c,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
checkConfigFile	checkConfigFile
checkFileWriteAccess	checkFileWriteAccess
checkPrimers	checkPrimers
checkTarget	checkTarget
cigarsToEvents	cigarsToEvents
comb_along	comb_along
cumsumw	cumsumw
decode	decode
defGR	defGR
experimentData	experimentData
experimentData,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
experimentData<-	experimentData-set
experimentData<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
extractEvents	extractEvents
extractEvents,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
findEOP	findEOP
findLQR	findLQR
findPD	findPD
flipRanges	flipRanges
fwdReads	fwdReads
fwdReads,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
fwdReads<-	fwdReads-set
fwdReads<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
fwdReadsType	fwdReadsType
fwdReadsType,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
fwdReadsType<-	fwdReadsType-set
fwdReadsType<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
geom_bezier	geom_bezier
getEventInfo	getEventInfo
getEvents	getEvents
get_left_primer	get_left_primer
get_right_primer	get_right_primer
get_seq	get_seq
goodAvgQuality	goodAvgQuality
goodBaseQuality	goodBaseQuality
is_hdr_strict	is_hdr_strict
length,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
locate_pr_start	locate_pr_start
lookupAlignment	lookupAlignment
lookupAlignment,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
makeAlignment	makeAlignment
metaplot_deletions	metaplot_deletions
metaplot_insertions	metaplot_insertions
metaplot_mismatches	metaplot_mismatches
names,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
pairToEvents	pairToEvents
plot_amplicon	plot_amplicon
plot_cuts	plot_cuts
plot_deletions	plot_deletions
plot_height	plot_height
plot_heterogeneity	plot_heterogeneity
plot_insertions	plot_insertions
plot_mismatches	plot_mismatches
plot_variants	plot_variants
readCounts	readCounts
readCounts,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
readCounts<-	readCounts-set
readCounts<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
revComp	revComp
rveReads	rveReads
rveReads,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
rveReads<-	rveReads-set
rveReads<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
rveReadsType	rveReadsType
rveReadsType,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
rveReadsType<-	rveReadsType-set
rveReadsType<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
stat_bezier	geom_bezier
unassignedCount	unassignedCount
unassignedCount,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
unassignedData	unassignedData
unassignedData,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
unassignedData<-	unassignedData-set
unassignedData<-,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
upperGroups	upperGroups
waffle	waffle
writeAlignments	writeAlignments
writeAlignments,AlignmentsExperimentSet-method	AlignmentsExperimentSet-class
[,AlignmentsExperimentSet,numeric,missing,missing-method	AlignmentsExperimentSet-class
