analyzeFeatures	analyzeFeatures
analyzeVariants	analyzeVariants
annotate	annotate
annotateSGVariants	annotateSGVariants
assays	assays
closed3p	slots
closed3p,SGVariantCounts-method	slots
closed3p,SGVariants-method	slots
closed3p<-	slots
closed3p<-,SGVariantCounts-method	slots
closed3p<-,SGVariants-method	slots
closed3pEvent	slots
closed3pEvent,SGVariantCounts-method	slots
closed3pEvent,SGVariants-method	slots
closed3pEvent<-	slots
closed3pEvent<-,SGVariantCounts-method	slots
closed3pEvent<-,SGVariants-method	slots
closed5p	slots
closed5p,SGVariantCounts-method	slots
closed5p,SGVariants-method	slots
closed5p<-	slots
closed5p<-,SGVariantCounts-method	slots
closed5p<-,SGVariants-method	slots
closed5pEvent	slots
closed5pEvent,SGVariantCounts-method	slots
closed5pEvent,SGVariants-method	slots
closed5pEvent<-	slots
closed5pEvent<-,SGVariantCounts-method	slots
closed5pEvent<-,SGVariants-method	slots
convertToSGFeatures	convertToSGFeatures
convertToTxFeatures	convertToTxFeatures
counts,SGFeatureCounts-method	assays
counts,SGVariantCounts-method	assays
counts<-,SGFeatureCounts-method	assays
counts<-,SGVariantCounts-method	assays
eventID	slots
eventID,SGVariantCounts-method	slots
eventID,SGVariants-method	slots
eventID<-	slots
eventID<-,SGVariantCounts-method	slots
eventID<-,SGVariants-method	slots
exonCompatible	exonCompatible
exportFeatures	exportFeatures
featureID	slots
featureID,Counts-method	slots
featureID,Paths-method	slots
featureID,SGFeatures-method	slots
featureID3p	slots
featureID3p,SGVariantCounts-method	slots
featureID3p,SGVariants-method	slots
featureID3p<-	slots
featureID3p<-,SGVariantCounts-method	slots
featureID3p<-,SGVariants-method	slots
featureID3pEvent	slots
featureID3pEvent,SGVariantCounts-method	slots
featureID3pEvent,SGVariants-method	slots
featureID3pEvent<-	slots
featureID3pEvent<-,SGVariantCounts-method	slots
featureID3pEvent<-,SGVariants-method	slots
featureID5p	slots
featureID5p,SGVariantCounts-method	slots
featureID5p,SGVariants-method	slots
featureID5p<-	slots
featureID5p<-,SGVariantCounts-method	slots
featureID5p<-,SGVariants-method	slots
featureID5pEvent	slots
featureID5pEvent,SGVariantCounts-method	slots
featureID5pEvent,SGVariants-method	slots
featureID5pEvent<-	slots
featureID5pEvent<-,SGVariantCounts-method	slots
featureID5pEvent<-,SGVariants-method	slots
featureID<-	slots
featureID<-,Counts-method	slots
featureID<-,Paths-method	slots
featureID<-,SGFeatures-method	slots
filterFeatures	filterFeatures
findOverlapsRanges	findOverlapsRanges
findSGVariants	findSGVariants
FPKM	assays
FPKM,SGFeatureCounts-method	assays
FPKM,SGVariantCounts-method	assays
FPKM<-	assays
FPKM<-,SGFeatureCounts-method	assays
from,Paths-method	slots
from,SGVariantCounts-method	slots
from<-	slots
from<-,Paths-method	slots
from<-,SGVariantCounts-method	slots
geneID	slots
geneID,Counts-method	slots
geneID,Paths-method	slots
geneID,SGFeatures-method	slots
geneID<-	slots
geneID<-,Counts-method	slots
geneID<-,Paths-method	slots
geneID<-,SGFeatures-method	slots
geneName	slots
geneName,Counts-method	slots
geneName,Features-method	slots
geneName,Paths-method	slots
geneName<-	slots
geneName<-,Counts-method	slots
geneName<-,Features-method	slots
geneName<-,Paths-method	slots
getBamInfo	getBamInfo
getSGFeatureCounts	getSGFeatureCounts
getSGFeatureCountsPerSample	getSGFeatureCountsPerSample
getSGVariantCounts	getSGVariantCounts
gr	gr
importTranscripts	importTranscripts
junctionCompatible	junctionCompatible
makeSGFeatureCounts	makeSGFeatureCounts
makeVariantNames	makeVariantNames
mergeTxFeatures	mergeTxFeatures
plotCoverage	plotCoverage
plotFeatures	plotFeatures
plotSpliceGraph	plotSpliceGraph
plotVariants	plotVariants
predictCandidatesInternal	predictCandidatesInternal
predictCandidatesTerminal	predictCandidatesTerminal
predictExonsInternal	predictExonsInternal
predictExonsTerminal	predictExonsTerminal
predictJunctions	predictJunctions
predictSpliced	predictSpliced
predictTxFeatures	predictTxFeatures
predictTxFeaturesPerSample	predictTxFeaturesPerSample
predictTxFeaturesPerStrand	predictTxFeaturesPerStrand
predictVariantEffects	predictVariantEffects
processTerminalExons	processTerminalExons
removeExonsIsolated	removeExonsIsolated
segmentID	slots
segmentID,Paths-method	slots
segmentID,SGVariantCounts-method	slots
segmentID<-	slots
segmentID<-,Paths-method	slots
segmentID<-,SGVariantCounts-method	slots
sgfc_ann	sgfc_ann
sgfc_pred	sgfc_pred
SGFeatureCounts	SGFeatureCounts
SGFeatures	SGFeatures
sgf_ann	sgf_ann
sgf_pred	sgf_pred
SGSegments	SGSegments
SGVariantCounts	SGVariantCounts
SGVariants	SGVariants
sgvc_ann	sgvc_ann
sgvc_ann_from_bam	sgvc_ann_from_bam
sgvc_pred	sgvc_pred
sgvc_pred_from_bam	sgvc_pred_from_bam
sgv_ann	sgv_ann
sgv_pred	sgv_pred
si	si
slots	slots
splice3p	slots
splice3p,SGFeatureCounts-method	slots
splice3p,SGFeatures-method	slots
splice3p,SGSegments-method	slots
splice3p<-	slots
splice3p<-,SGFeatureCounts-method	slots
splice3p<-,SGFeatures-method	slots
splice3p<-,SGSegments-method	slots
splice5p	slots
splice5p,SGFeatureCounts-method	slots
splice5p,SGFeatures-method	slots
splice5p,SGSegments-method	slots
splice5p<-	slots
splice5p<-,SGFeatureCounts-method	slots
splice5p<-,SGFeatures-method	slots
splice5p<-,SGSegments-method	slots
splicesiteOverlap	splicesiteOverlap
to,Paths-method	slots
to,SGVariantCounts-method	slots
to<-	slots
to<-,Paths-method	slots
to<-,SGVariantCounts-method	slots
tx	tx
TxFeatures	TxFeatures
txf_ann	txf_ann
txf_pred	txf_pred
txName	slots
txName,Counts-method	slots
txName,Features-method	slots
txName,Paths-method	slots
txName<-	slots
txName<-,Counts-method	slots
txName<-,Features-method	slots
txName<-,Paths-method	slots
type,Counts-method	slots
type,Features-method	slots
type,Paths-method	slots
type<-	slots
type<-,Counts-method	slots
type<-,Features-method	slots
type<-,Paths-method	slots
updateObject	updateObject
updateObject,SGVariantCounts-method	updateObject
updateObject,SGVariants-method	updateObject
variantFreq	assays
variantFreq,SGVariantCounts-method	assays
variantFreq<-	assays
variantFreq<-,SGVariantCounts-method	assays
variantID	slots
variantID,SGVariantCounts-method	slots
variantID,SGVariants-method	slots
variantID<-	slots
variantID<-,SGVariantCounts-method	slots
variantID<-,SGVariants-method	slots
variantName	slots
variantName,SGVariantCounts-method	slots
variantName,SGVariants-method	slots
variantName<-	slots
variantName<-,SGVariantCounts-method	slots
variantName<-,SGVariants-method	slots
variantType	slots
variantType,SGVariantCounts-method	slots
variantType,SGVariants-method	slots
variantType<-	slots
variantType<-,SGVariantCounts-method	slots
variantType<-,SGVariants-method	slots
