NxtIRFcore-package	NxtIRFcore-package
apply_filters	Run_NxtIRF_Filters
ASE-methods	ASE-methods
as_egg_ggplot	Plot_Coverage
BAM2COV	IRFinder
BuildReference	BuildReference
BuildReference_Full	BuildReference
cbind,NxtSE-method	NxtSE-class
coerce,SummarizedExperiment,NxtSE-method	NxtSE-class
CollateData	CollateData
CoordToGR	CoordToGR
Coverage	Coverage
covfile	NxtSE-class
covfile,NxtSE-method	NxtSE-class
covfile<-	NxtSE-class
covfile<-,NxtSE-method	NxtSE-class
DESeq_ASE	ASE-methods
DoubleExpSeq_ASE	ASE-methods
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-NxtIRF-data	example-NxtIRF-data
Find_Bams	Find_Samples
Find_FASTQ	Find_Samples
Find_IRFinder_Output	Find_Samples
Find_Samples	Find_Samples
GetCoverage	Coverage
GetCoverageBins	Coverage
GetCoverageRegions	Coverage
GetCoverage_DF	Coverage
GetNonPolyARef	BuildReference
GetReferenceResource	BuildReference
get_default_filters	Run_NxtIRF_Filters
IRFinder	IRFinder
IsCOV	IsCOV
limma_ASE	ASE-methods
MakeSE	MakeSE
make_diagonal	make_plot_data
make_matrix	make_plot_data
make_plot_data	make_plot_data
Mappability-methods	Mappability-methods
Mappability_CalculateExclusions	Mappability-methods
Mappability_GenReads	Mappability-methods
NxtFilter	NxtFilter-class
NxtFilter-class	NxtFilter-class
NxtIRF_example_bams	example-NxtIRF-data
NxtIRF_example_NxtSE	example-NxtIRF-data
NxtSE	NxtSE-class
NxtSE-class	NxtSE-class
NxtSE-methods	NxtSE-class
Plot_Coverage	Plot_Coverage
Plot_Genome	Plot_Coverage
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_NxtIRF_Filters
Run_NxtIRF_Filters	Run_NxtIRF_Filters
sampleQC	NxtSE-class
sampleQC,NxtSE-method	NxtSE-class
sampleQC<-	NxtSE-class
sampleQC<-,NxtSE-method	NxtSE-class
STAR-methods	STAR-methods
STAR_align_experiment	STAR-methods
STAR_align_fastq	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
[,NxtSE,ANY,ANY,ANY-method	NxtSE-class
[<-,NxtSE,ANY,ANY,NxtSE-method	NxtSE-class
