SpliceWiz-package	SpliceWiz-package
addPSI_edgeR	ASE-GLM-edgeR
applyFilters	Run_SpliceWiz_Filters
ASE-GLM-edgeR	ASE-GLM-edgeR
ASE-methods	ASE-methods
ASEFilter	ASEFilter-class
ASEFilter-class	ASEFilter-class
ASE_DESeq	ASE-methods
ASE_DoubleExpSeq	ASE-methods
ASE_edgeR	ASE-methods
ASE_edgeR_timeseries	ASE-methods
ASE_limma	ASE-methods
ASE_limma_timeseries	ASE-methods
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
condition	covPlotObject-class
condition,covPlotObject-method	covPlotObject-class
coord2GR	coord2GR
covDataObject-class	covDataObject-class
Coverage	Coverage
covfile	NxtSE-class
covfile,NxtSE-method	NxtSE-class
covfile<-	NxtSE-class
covfile<-,NxtSE-method	NxtSE-class
covPlotly-class	covPlotly-class
covPlotObject-class	covPlotObject-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
extract_gene_ids_for_GO	Gene-ontology-methods
findBAMS	findSamples
findFASTQ	findSamples
findSamples	findSamples
findSpliceWizOutput	findSamples
fitASE_edgeR	ASE-GLM-edgeR
fitASE_edgeR_custom	ASE-GLM-edgeR
Gene-ontology-methods	Gene-ontology-methods
generateSyntheticReads	Mappability-methods
getAvailableGO	Build-Reference-methods
getCoverage	Coverage
getCoverageBins	Coverage
getCoverageData	covDataObject-class
getCoverageRegions	Coverage
getCoverage_DF	Coverage
getDefaultFilters	Run_SpliceWiz_Filters
getExonRanges	covPlotly-class
getExonRanges,covPlotly-method	covPlotly-class
getGenomeData	covDataObject-class
getNonPolyARef	Build-Reference-methods
getPlotObject	covPlotObject-class
getResources	Build-Reference-methods
goASE	Gene-ontology-methods
goGenes	Gene-ontology-methods
Graphics-User-Interface	Graphics-User-Interface
GUI	Graphics-User-Interface
isCOV	isCOV
junc_counts	NxtSE-class
junc_counts,NxtSE-method	NxtSE-class
junc_counts_uns	NxtSE-class
junc_counts_uns,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
plotAnnoTrack	covDataObject-class
plotCoverage	plotCoverage
plotGenome	plotCoverage
plotGO	Gene-ontology-methods
plotView	covPlotObject-class
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
row_gr	NxtSE-class
row_gr,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
setResolution	covPlotly-class
setResolution,covPlotly-method	covPlotly-class
setSWthreads	setSWthreads
showEvents	covDataObject-class
showEvents,covDataObject-method	covDataObject-class
showExons	covPlotly-class
showExons,covPlotly-method	covPlotly-class
sourcePath	NxtSE-class
sourcePath,NxtSE-method	NxtSE-class
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_buildGenome	STAR-methods
STAR_buildRef	STAR-methods
STAR_loadGenomeGTF	STAR-methods
STAR_mappability	STAR-methods
STAR_version	STAR-methods
subset_EventNames_by_GO	Gene-ontology-methods
testASE_edgeR	ASE-GLM-edgeR
theme_white	theme_white
theme_white_legend	theme_white
theme_white_legend_plot_track	theme_white
tracks	covPlotObject-class
tracks,covPlotObject-method	covPlotObject-class
update_NxtSE	NxtSE-class
update_NxtSE,NxtSE-method	NxtSE-class
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
viewGO	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
