SplicingGraphs-package	SplicingGraphs-package
ASCODE2DESC	bubbles-methods
assignReads	assignReads
bubbles	bubbles-methods
bubbles,ANY-method	bubbles-methods
bubbles,IntegerList-method	bubbles-methods
bubbles,SplicingGraphs-method	bubbles-methods
bubbles-methods	bubbles-methods
class:GeneModel	SplicingGraphs-class
class:SplicingGraphs	SplicingGraphs-class
countReads	countReads-methods
countReads,SplicingGraphs-method	countReads-methods
countReads-methods	countReads-methods
elementLengths,SplicingGraphs-method	SplicingGraphs-class
GeneModel-class	SplicingGraphs-class
indeg	sgedges-methods
indeg,ANY-method	sgedges-methods
indeg,DataFrame-method	sgedges-methods
intronsByTranscript,SplicingGraphs-method	sgedgesByGene-methods
length,SplicingGraphs-method	SplicingGraphs-class
names,SplicingGraphs-method	SplicingGraphs-class
outdeg	sgedges-methods
outdeg,ANY-method	sgedges-methods
outdeg,DataFrame-method	sgedges-methods
plot,SplicingGraphs,ANY-method	sgraph-methods
plotTranscripts	plotTranscripts-methods
plotTranscripts,GRangesList-method	plotTranscripts-methods
plotTranscripts,SplicingGraphs-method	plotTranscripts-methods
plotTranscripts,TranscriptDb-method	plotTranscripts-methods
plotTranscripts-methods	plotTranscripts-methods
removeReads	assignReads
rsgedges	rsgedgesByGene-methods
rsgedgesByGene	rsgedgesByGene-methods
rsgedgesByGene,SplicingGraphs-method	rsgedgesByGene-methods
rsgedgesByGene-methods	rsgedgesByGene-methods
rsgedgesByTranscript	rsgedgesByGene-methods
rsgedgesByTranscript,SplicingGraphs-method	rsgedgesByGene-methods
rsgraph	rsgedgesByGene-methods
seqinfo,GeneModel-method	SplicingGraphs-class
seqinfo,SplicingGraphs-method	SplicingGraphs-class
seqnames,GeneModel-method	SplicingGraphs-class
seqnames,SplicingGraphs-method	SplicingGraphs-class
sgedges	sgedges-methods
sgedges,SplicingGraphs-method	sgedges-methods
sgedges-methods	sgedges-methods
sgedges2	rsgedgesByGene-methods
sgedgesByGene	sgedgesByGene-methods
sgedgesByGene,SplicingGraphs-method	sgedgesByGene-methods
sgedgesByGene-methods	sgedgesByGene-methods
sgedgesByTranscript	sgedgesByGene-methods
sgedgesByTranscript,SplicingGraphs-method	sgedgesByGene-methods
sgnodes	sgedges-methods
sgnodes,data.frame-method	sgedges-methods
sgnodes,DataFrame-method	sgedges-methods
sgnodes,IntegerList-method	sgedges-methods
sgnodes,SplicingGraphs-method	sgedges-methods
sgraph	sgraph-methods
sgraph,ANY-method	sgraph-methods
sgraph,data.frame-method	sgraph-methods
sgraph,DataFrame-method	sgraph-methods
sgraph,igraph-method	sgraph-methods
sgraph-methods	sgraph-methods
sgraph2	rsgedgesByGene-methods
show,SplicingGraphs-method	SplicingGraphs-class
slideshow	sgraph-methods
SplicingGraphs	SplicingGraphs-class
SplicingGraphs,GRangesList-method	SplicingGraphs-class
SplicingGraphs,TranscriptDb-method	SplicingGraphs-class
SplicingGraphs-class	SplicingGraphs-class
strand,GeneModel-method	SplicingGraphs-class
strand,SplicingGraphs-method	SplicingGraphs-class
toy_data	toy_data
toy_genes_gff	toy_data
toy_overlaps	toy_data
toy_reads_bam	toy_data
toy_reads_sam	toy_data
TSPC	TSPCsg
TSPCsg	TSPCsg
txpath	txpath-methods
txpath,GRangesList-method	txpath-methods
txpath,SplicingGraphs-method	txpath-methods
txpath-methods	txpath-methods
txweight	txpath-methods
txweight,SplicingGraphs-method	txpath-methods
txweight<-	txpath-methods
txweight<-,SplicingGraphs-method	txpath-methods
uninformativeSSids	rsgedgesByGene-methods
uninformativeSSids,ANY-method	rsgedgesByGene-methods
uninformativeSSids,DataFrame-method	rsgedgesByGene-methods
unlist,SplicingGraphs-method	SplicingGraphs-class
[,SplicingGraphs,ANY,ANY-method	SplicingGraphs-class
[[,SplicingGraphs,ANY,ANY-method	SplicingGraphs-class
