spliceSites-package	spliceSites-package
aaGapSites-class	aaGapSites-class
addGeneAligns	addGeneAligns
addGeneAligns,gapSites-method	addGeneAligns
addGeneAligns-method	addGeneAligns
addGenomeData	addGenomeData-ExpressionSet
addGenomeData,ExpressionSet,DNAStringSet,refJunctions-method	addGenomeData-ExpressionSet
addGenomeData,gapSites,DNAStringSet,refJunctions-method	addGenomeData-gapSites
addGenomeData-method	addGenomeData-ExpressionSet
addHbond	addHbond
addHbond,cdRanges-method	addHbond
addHbond,gapSites-method	addHbond
addHbond-methods	addHbond
addKeyTable	keyProfiler-class
addKeyTable,keyProfiler-method	keyProfiler-class
addKeyTable-methods	keyProfiler-class
addMaxEnt	addMaxEnt
addMaxEnt,gapSites-method	addMaxEnt
addMaxEnt-methods	addMaxEnt
alignGapList	getGapSites
alt_left_ranks	alt_X_ranks
alt_left_ranks,gapSites-method	alt_X_ranks
alt_left_ranks-methods	alt_X_ranks
alt_ranks	alt_X_ranks
alt_ranks,gapSites-method	alt_X_ranks
alt_ranks-methods	alt_X_ranks
alt_right_ranks	alt_X_ranks
alt_right_ranks,gapSites-method	alt_X_ranks
alt_right_ranks-method	alt_X_ranks
annGapSites-class	annGapSites-class
annotate	annotation
annotate,ExpressionSet,refJunctions-method	annotate-ExpressionSet
annotate,gapSites,refJunctions-method	annotation
annotate-methods	annotation
annotation	annotation
annotation,gapSites-method	annotation
annotation-methods	annotation
annotation<-	annotation
annotation<-,gapSites,ANY-method	annotation
annotation<-,gapSites,refJunctions-method	annotation
annotation<--methods	annotation
appendKeyTable	keyProfiler-class
appendKeyTable,keyProfiler-method	keyProfiler-class
appendKeyTable-methods	keyProfiler-class
as.data.frame-methods	as.data.frame-methods
as.data.frame.cRanges	cRanges-class
as.data.frame.gapSites	gapSites-class
basedir,hbond-method	hbond-class
basedir,maxEnt-method	maxEnt-class
basedir<-,hbond-method	hbond-class
basedir<-,maxEnt-method	maxEnt-class
c,caRanges-method	caRanges-class
c,cdRanges-method	cdRanges-class
c,cRanges-method	cRanges-class
c,gapSites-method	gapSites-class
c-methods	c-methods
caRanges-class	caRanges-class
cdRanges-class	cdRanges-class
count	cRanges-class
count,cRanges-method	cRanges-class
count-methods	cRanges-class
countByGeneName	countByGeneName
cRanges-class	cRanges-class
dim,cRanges-method	cRanges-class
dim,gapSites-method	gapSites-class
dim-methods	dim-methods
dnaGapSites	gapSites
dnaGapSites,gapSites,DNAStringSet-method	gapSites-class
dnaGapSites-class	dnaGapSites-class
dnaGapSites-methods	gapSites
dnaRanges	dnaRanges
dnaRanges,cRanges,DNAStringSet,logical-method	dnaRanges
dnaRanges,cRanges,DNAStringSet,missing-method	dnaRanges
dnaRanges-methods	dnaRanges
do_group_align_data	gapSites-class
end,cRanges-method	cRanges-class
extractByGeneName	extractByGeneName
extractByGeneName,cRanges,ANY-method	extractByGeneName
extractByGeneName,cRanges-method	extractByGeneName
extractByGeneName,gapSites,ANY-method	extractByGeneName
extractByGeneName,gapSites-method	extractByGeneName
extractByGeneName-methods	extractByGeneName
extractRange	extractRange
extractRange,cRanges-method	extractRange
extractRange,gapSites-method	extractRange
extractRange-methods	extractRange
gapSites	gapSites
gapSites-class	gapSites-class
getAnnStrand	gapSites-class
getAnnStrand,gapSites-method	gapSites-class
getAnnStrand-methods	gapSites-class
getGapSites	getGapSites
getKeyTable	keyProfiler-class
getKeyTable,keyProfiler-method	keyProfiler-class
getKeyTable-methods	keyProfiler-class
getMeStrand	addMaxEnt
getMeStrand,gapSites-method	addMaxEnt
getMeStrand-methods	addMaxEnt
getProfile	gapSites-class
getProfile,gapSites-method	gapSites-class
getProfile-methods	gapSites-class
getSequence	cdRanges-class
getSequence,caRanges-method	caRanges-class
getSequence,cdRanges-method	cdRanges-class
getSequence-methods	cdRanges-class
gptm	gapSites-class
gptm,gapSites-method	gapSites-class
gptm-methods	gapSites-class
hbond	hbond-class
hbond,hbond-method	hbond-class
hbond-class	hbond-class
hbond-methods	hbond-class
head,aaGapSites-method	aaGapSites-class
head,caRanges-method	caRanges-class
head,cdRanges-method	cdRanges-class
head,cRanges-method	cRanges-class
head,dnaGapSites-method	dnaGapSites-class
head,gapSites-method	gapSites-class
head-methods	head-methods
id	cRanges-class
id,cRanges-method	cRanges-class
id-methods	cRanges-class
initialize,cdRanges-method	cdRanges-class
initialize,cRanges-method	cRanges-class
initialize,keyProfiler-method	keyProfiler-class
initialize,SpliceCountSet-method	SpliceCountSet-class
initialize-methods	initialize-methods
keyProfiler-class	keyProfiler-class
lCodons	xCodons
lCodons,cRanges-method	xCodons
lCodons-methods	xCodons
lend	gapSites-class
lend,gapSites-method	gapSites-class
lend-methods	gapSites-class
lJunc	xJunc
lJunc,gapSites-method	xJunc
lJunc-methods	xJunc
lJuncStrand	xJuncStrand
lJuncStrand,gapSites-method	xJuncStrand
lJuncStrand-methods	xJuncStrand
load.hbond	hbond-class
load.maxEnt	maxEnt-class
lrCodons	lrCodons
lrCodons,gapSites-method	lrCodons
lrCodons-methods	lrCodons
lrJunc	xJunc
lrJunc,gapSites-method	xJunc
lrJunc-methods	xJunc
lrJuncStrand	xJuncStrand
lrJuncStrand,gapSites-method	xJuncStrand
lrJuncStrand-methods	xJuncStrand
lstart	gapSites-class
lstart,gapSites-method	gapSites-class
lstart-methods	gapSites-class
maxEnt-class	maxEnt-class
merge-methods	merge-methods
merge.gapSites	gapSites-class
nAlignGaps	gapSites-class
nAlignGaps,gapSites-method	gapSites-class
nAlignGaps-methods	gapSites-class
nAligns	gapSites-class
nAligns,gapSites-method	gapSites-class
nAligns-methods	gapSites-class
overlap_genome	gapSites-class
plotGeneAlignDepth	plotGeneAlignDepth
plotGeneAlignDepth,bamReader-method	plotGeneAlignDepth
plotGeneAlignDepth-methods	plotGeneAlignDepth
plot_diff	annGapSites-class
plot_diff,annGapSites-method	annGapSites-class
plot_diff-methods	annGapSites-class
plot_diff_ranks	alt_X_ranks
plot_diff_ranks,gapSites-method	alt_X_ranks
plot_diff_ranks-methods	alt_X_ranks
rangeByGeneName	rangeByGeneName
rCodons	xCodons
rCodons,cRanges-method	xCodons
rCodons-methods	xCodons
readCuffGeneFpkm	readCuffGeneFpkm
readExpSet	readExpSet
readMergedBamGaps	readMergedBamGaps
readTabledBamGaps	readTabledBamGaps
rend	gapSites-class
rend,gapSites-method	gapSites-class
rend-methods	gapSites-class
resize_left	trim
resize_left,gapSites-method	trim
resize_left-methods	trim
resize_right	trim
resize_right,gapSites-method	trim
resize_right-methods	trim
rJunc	xJunc
rJunc,gapSites-method	xJunc
rJunc-methods	xJunc
rJuncStrand	xJuncStrand
rJuncStrand,gapSites-method	xJuncStrand
rJuncStrand-methods	xJuncStrand
rpmg	gapSites-class
rpmg,gapSites-method	gapSites-class
rpmg-methods	gapSites-class
rstart	gapSites-class
rstart,gapSites-method	gapSites-class
rstart-methods	gapSites-class
saveMaxEnt	maxEnt-class
saveMaxEnt,maxEnt-method	maxEnt-class
saveMaxEnt-methods	maxEnt-class
score3	maxEnt-class
score3,maxEnt-method	maxEnt-class
score3-methods	maxEnt-class
score5	maxEnt-class
score5,maxEnt-method	maxEnt-class
score5-methods	maxEnt-class
scoreSeq3	maxEnt-class
scoreSeq3,maxEnt-method	maxEnt-class
scoreSeq3-methods	maxEnt-class
scoreSeq5	maxEnt-class
scoreSeq5,maxEnt-method	maxEnt-class
scoreSeq5-methods	maxEnt-class
seqid	gapSites-class
seqid,cRanges-method	cRanges-class
seqid,gapSites-method	gapSites-class
seqid-methods	gapSites-class
seqlogo	seqlogo
seqlogo,cdRanges-method	seqlogo
seqlogo,dnaGapSites-method	dnaGapSites-class
seqlogo-methods	seqlogo
setMeStrand	addMaxEnt
setMeStrand,gapSites-method	addMaxEnt
setMeStrand-methods	addMaxEnt
show,aaGapSites-method	aaGapSites-class
show,cRanges-method	cRanges-class
show,dnaGapSites-method	dnaGapSites-class
show,gapSites-method	gapSites-class
silic_tryp	silic_tryp
sortTable	cRanges-class
sortTable,cRanges-method	cRanges-class
sortTable,gapSites-method	gapSites-class
sortTable-methods	sortTable-methods
SpliceCountSet-class	SpliceCountSet-class
spliceSites	spliceSites-package
start,cRanges-method	cRanges-class
strand	cRanges-class
strand,cRanges-method	cRanges-class
strand,gapSites-method	gapSites-class
strand-methods	cRanges-class
strand<-,gapSites-method	gapSites-class
translate	cdRanges-class
translate,cdRanges-method	cdRanges-class
translate,dnaGapSites-method	dnaGapSites-class
translate-methods	cdRanges-class
trim_left	trim
trim_left,gapSites-method	trim
trim_left-methods	trim
trim_right	trim
trim_right,gapSites-method	trim
trim_right-methods	trim
truncateSeq	truncateSeq
truncateSeq,aaGapSites-method	truncateSeq
truncateSeq,caRanges-method	truncateSeq
truncateSeq-methods	truncateSeq
truncate_seq	truncate_seq
trypsinCleave	trypsinCleave
trypsinCleave,aaGapSites-method	trypsinCleave
trypsinCleave,caRanges-method	trypsinCleave
trypsinCleave-methods	trypsinCleave
uniqueJuncAnn	uniqueJuncAnn
uniqueJuncAnn,ExpressionSet,refJunctions-method	uniqueJuncAnn
uniqueJuncAnn-methods	uniqueJuncAnn
width,cRanges-method	cRanges-class
write.annDNA.tables	gapSites-class
write.annDNA.tables,gapSites,DNAStringSet,character-method	gapSites-class
write.annDNA.tables-methods	gapSites-class
write.files	write.files
write.files,aaGapSites-method	aaGapSites-class
write.files,caRanges-method	caRanges-class
write.files-methods	write.files
[,gapSites,ANY,ANY,ANY-method	gapSites-class
[-methods	z[-methods
