SpliceWiz-package	SpliceWiz-package
applyFilters	Run_SpliceWiz_Filters
ASE-methods	ASE-methods
ASEFilter	ASEFilter-class
ASEFilter-class	ASEFilter-class
ASE_DESeq	ASE-methods
ASE_DoubleExpSeq	ASE-methods
ASE_limma	ASE-methods
ASE_satuRn	ASE-methods
as_ggplot_cov	plotCoverage
BAM2COV	processBAM
Build-Reference-methods	Build-Reference-methods
buildFullRef	Build-Reference-methods
buildRef	Build-Reference-methods
calculateMappability	Mappability-methods
cbind,NxtSE-method	NxtSE-class
coerce,SummarizedExperiment,NxtSE-method	NxtSE-class
collateData	collateData
coord2GR	coord2GR
Coverage	Coverage
covfile	NxtSE-class
covfile,NxtSE-method	NxtSE-class
covfile<-	NxtSE-class
covfile<-,NxtSE-method	NxtSE-class
down_exc	NxtSE-class
down_exc,NxtSE-method	NxtSE-class
down_exc<-	NxtSE-class
down_exc<-,NxtSE-method	NxtSE-class
down_inc	NxtSE-class
down_inc,NxtSE-method	NxtSE-class
down_inc<-	NxtSE-class
down_inc<-,NxtSE-method	NxtSE-class
example-SpliceWiz-data	example-SpliceWiz-data
findBAMS	findSamples
findFASTQ	findSamples
findSamples	findSamples
findSpliceWizOutput	findSamples
generateSyntheticReads	Mappability-methods
getCoverage	Coverage
getCoverageBins	Coverage
getCoverageRegions	Coverage
getCoverage_DF	Coverage
getDefaultFilters	Run_SpliceWiz_Filters
getNonPolyARef	Build-Reference-methods
getResources	Build-Reference-methods
Graphics-User-Interface	Graphics-User-Interface
GUI	Graphics-User-Interface
isCOV	isCOV
junc_counts	NxtSE-class
junc_counts,NxtSE-method	NxtSE-class
junc_gr	NxtSE-class
junc_gr,NxtSE-method	NxtSE-class
junc_PSI	NxtSE-class
junc_PSI,NxtSE-method	NxtSE-class
makeMatrix	make_plot_data
makeMeanPSI	make_plot_data
makeSE	makeSE
make_plot_data	make_plot_data
Mappability-methods	Mappability-methods
NxtSE	NxtSE-class
NxtSE-class	NxtSE-class
NxtSE-methods	NxtSE-class
plotCoverage	plotCoverage
plotGenome	plotCoverage
processBAM	processBAM
rbind,NxtSE-method	NxtSE-class
realize_NxtSE	NxtSE-class
realize_NxtSE,NxtSE-method	NxtSE-class
ref	NxtSE-class
ref,NxtSE-method	NxtSE-class
runFilter	Run_SpliceWiz_Filters
Run_SpliceWiz_Filters	Run_SpliceWiz_Filters
sampleQC	NxtSE-class
sampleQC,NxtSE-method	NxtSE-class
sampleQC<-	NxtSE-class
sampleQC<-,NxtSE-method	NxtSE-class
setSWthreads	setSWthreads
spliceWiz	Graphics-User-Interface
SpliceWiz_example_bams	example-SpliceWiz-data
SpliceWiz_example_NxtSE	example-SpliceWiz-data
STAR-methods	STAR-methods
STAR_alignExperiment	STAR-methods
STAR_alignReads	STAR-methods
STAR_buildRef	STAR-methods
STAR_mappability	STAR-methods
STAR_version	STAR-methods
theme_white	theme_white
theme_white_legend	theme_white
theme_white_legend_plot_track	theme_white
up_exc	NxtSE-class
up_exc,NxtSE-method	NxtSE-class
up_exc<-	NxtSE-class
up_exc<-,NxtSE-method	NxtSE-class
up_inc	NxtSE-class
up_inc,NxtSE-method	NxtSE-class
up_inc<-	NxtSE-class
up_inc<-,NxtSE-method	NxtSE-class
View-Reference-methods	View-Reference-methods
viewASE	View-Reference-methods
viewExons	View-Reference-methods
viewGenes	View-Reference-methods
viewIntrons	View-Reference-methods
viewIR	View-Reference-methods
viewIR_NMD	View-Reference-methods
viewProteins	View-Reference-methods
viewTranscripts	View-Reference-methods
[,NxtSE,ANY,ANY,ANY-method	NxtSE-class
[<-,NxtSE,ANY,ANY,NxtSE-method	NxtSE-class
