%in2%	InternalFunctions
AllEvents_RNASeq	AllEvents_RNASeq
AllEvents_RNASeq_MP	AllEvents_RNASeq_MP
all_simple_paths2	InternalFunctions
AnnEventsFunc	InternalFunctions
annotate2	InternalFunctions
annotateEvents	InternalFunctions
annotateEventsMultipath	InternalFunctions
AnnotateEvents_KLL	InternalFunctions
AnnotateEvents_RNASeq	InternalFunctions
AnnotateEvents_RNASeq_MultiPath	InternalFunctions
annotateFeatures2	InternalFunctions
ArrayDatamultipath	ArrayDatamultipath
ArraysData	ArraysData
calcBootstrapPSI	InternalFunctions
calculateCorrelationTest	InternalFunctions
callGRseq_parallel	InternalFunctions
callPrimer3	InternalFunctions
callPrimer3probes	InternalFunctions
call_get_table_Bootstrap	InternalFunctions
CDFfromGTF	CDFfromGTF
CDFfromGTF_Multipath	CDFfromGTF_Multipath
checkContrastDesignMatrices	InternalFunctions
ClassifyEvents	InternalFunctions
co2str	InternalFunctions
constructGRangesFromRanges	InternalFunctions
constructPaired	InternalFunctions
convertToSGFeatures2	InternalFunctions
CreateExSmatrix	CreateExSmatrix
CreateSequenceforProbe	InternalFunctions
dgl	InternalFunctions
dimMatrixFix	InternalFunctions
estimateAbsoluteConc	InternalFunctions
estimateAbsoluteConcmultipath	InternalFunctions
estimateAbsoluteConc_boot	InternalFunctions
estimatePSI	InternalFunctions
EventDetection	EventDetection
EventDetectionAnn	EventDetectionAnn
EventDetectionMultipath	EventDetectionMultipath
EventDetection_transcriptome	EventDetection_transcriptome
EventPointer	EventPointer
EventPointerBAM_IGV	EventPointerBAM_IGV
EventPointerStats_BAM	EventPointerStats_BAM
EventPointer_Bootstraps	EventPointer_Bootstraps
EventPointer_IGV	EventPointer_IGV
EventPointer_RNASeq	EventPointer_RNASeq
EventPointer_RNASeq_TranRef	EventPointer_RNASeq_TranRef
EventPointer_RNASeq_TranRef_IGV	EventPointer_RNASeq_TranRef_IGV
EventsDetection_BAM	EventsDetection_BAM
Events_ReClassification	Events_ReClassification
EventXtrans	EventXtrans
exonCompatible	InternalFunctions
exonCoverage	InternalFunctions
expandUnstrandedRanges	InternalFunctions
extractSplicesitesFromJunctions	InternalFunctions
filterimagine	InternalFunctions
filterIntrons	InternalFunctions
findOverlapsRanges	InternalFunctions
findPotencialExons	InternalFunctions
FindPrimers	FindPrimers
findTriplets	InternalFunctions
findTriplets2	InternalFunctions
Fit	Fit
fitgl	InternalFunctions
flat2Cdf	InternalFunctions
fragExonIntron	InternalFunctions
fullExons	InternalFunctions
generateWarningMessage	InternalFunctions
genreverse	InternalFunctions
getBamInfo	InternalFunctions
getBamInfoPerSample	InternalFunctions
getbootstrapdata	getbootstrapdata
getCountMatrix	InternalFunctions
GetCounts	InternalFunctions
GetCountsMP	InternalFunctions
getDistanceseachPath	InternalFunctions
getDominants2	InternalFunctions
getDominantsFor	InternalFunctions
getDominantsRev	InternalFunctions
getEventMultiPaths	InternalFunctions
getEventPaths	InternalFunctions
getExonsFullSignal	InternalFunctions
getFinalExons	InternalFunctions
getgeneraldata	InternalFunctions
GetIGVPaths	InternalFunctions
getInfo	InternalFunctions
getPathCounts	InternalFunctions
getPathCountsMP	InternalFunctions
getPathFPKMs	InternalFunctions
getPathFPKMsMP	InternalFunctions
getpij	InternalFunctions
getPSI	InternalFunctions
getPSImultipath	InternalFunctions
GetPSI_FromTranRef	GetPSI_FromTranRef
getPSI_RNASeq	InternalFunctions
getPSI_RNASeq_boot	getPSI_RNASeq_boot
getPSI_RNASeq_MultiPath	InternalFunctions
getRandomFlow	InternalFunctions
getrankexons	InternalFunctions
getranksequence	InternalFunctions
getSGFeatureCounts	InternalFunctions
getSGFeatureCountsTotal	InternalFunctions
get_beta	InternalFunctions
get_table	InternalFunctions
get_table_Bootstrap	InternalFunctions
get_YB	InternalFunctions
globalWhich	InternalFunctions
GseaApproach	InternalFunctions
hyperGeometricApproach	InternalFunctions
hyperMatrixRes	InternalFunctions
IHsummarization	InternalFunctions
includeaexons	InternalFunctions
InternalFunctions	InternalFunctions
junctionCompatible	InternalFunctions
listCHRFileCount	InternalFunctions
listCHRFilePredict	InternalFunctions
MatrixRes	InternalFunctions
mclapplyPSI_Bootstrap	InternalFunctions
mergeExonsTerminal2	InternalFunctions
modFindOverlap	InternalFunctions
myphyper	InternalFunctions
MyPrimers	MyPrimers
MyPrimers_taqman	MyPrimers_taqman
pdist2	InternalFunctions
pgl	InternalFunctions
poissonBinomialApproach	InternalFunctions
predictCandidatesInternal	InternalFunctions
predictCandidatesTerminal	InternalFunctions
predictExonsInternal	InternalFunctions
predictExonsTerminal	InternalFunctions
predictJunctions	InternalFunctions
predictSpliced	InternalFunctions
predictTxFeatures	InternalFunctions
predictTxFeaturesTotal	InternalFunctions
PrepareBam_EP	PrepareBam_EP
PrepareCountData	InternalFunctions
PrepareOutput	InternalFunctions
PrepareProbes	InternalFunctions
PrimerSequenceCommonFor	InternalFunctions
PrimerSequenceCommonRev	InternalFunctions
PrimerSequenceGeneral	InternalFunctions
PrimerSequenceTwo	InternalFunctions
ProbesSequence	InternalFunctions
processCounts	InternalFunctions
processFeatures2	InternalFunctions
Protein_Domain_Enrichment	Protein_Domain_Enrichment
PSIss	PSIss
PSI_boots	PSI_boots
PSI_Statistic	PSI_Statistic
pvalue_incr_PSI	InternalFunctions
qdgl	InternalFunctions
qgl	InternalFunctions
readGapPair	InternalFunctions
reclasify_intern	InternalFunctions
reClassificationIntern	InternalFunctions
ResulTable	ResulTable
rgl	InternalFunctions
sacartranscritos	InternalFunctions
sampleWhichCount	InternalFunctions
sampleWhichPredict	InternalFunctions
SF_Prediction	SF_Prediction
SG_creation	InternalFunctions
SG_creation_fast	InternalFunctions
SG_creation_RNASeq	InternalFunctions
SG_Info	InternalFunctions
SG_reclassify	SG_reclassify
SG_RNASeq	SG_RNASeq
significanceFunction	InternalFunctions
sort_exons	InternalFunctions
speedglm.wfit2	InternalFunctions
splicesiteCounts	InternalFunctions
splicesiteOverlap	InternalFunctions
togroup0	InternalFunctions
transfromedge	InternalFunctions
TxD	TxD
uniquefast	InternalFunctions
validationParameters	InternalFunctions
Wilcoxon.z.matrix	InternalFunctions
WilcoxonApproach	InternalFunctions
WriteGTF	InternalFunctions
WriteGTF_RNASeq	InternalFunctions
