addVar	addVar
adjustPeaks	adjustPeaks
adjustPeaks,GRangesList-method	adjustPeaks
adjustPeaks-methods	adjustPeaks
as.matrix,distGPS-method	distGPS-class
bg3	bg3
bg3.tab	bg3
bg3names	bg3
boostMDS	boostMDS
clusGPS	clusGPS
clusGPS,distGPS,mds-method	clusGPS
clusGPS-class	clusGPS-class
clusGPS-method	clusGPS-class
clusGPS-methods	clusGPS
clusNames	clusGPS
clusNames,clusGPS-method	clusGPS
clusterID	clusGPS
clusterID,clusGPS-method	clusGPS
combineGenesMatrix	combineGenesMatrix
contour2dDP	clusGPS
d	s2
d.origs	s2
d2	s2
d3	s2
diffFactors	diffFactors
diffFactors-methods	diffFactors
diffGenes	diffGenes
diffGenes-methods	diffGenes
distGPS	distGPS
distGPS,data.frame-method	distGPS
distGPS,GRangesList-method	distGPS
distGPS,matrix-method	distGPS
distGPS-class	distGPS-class
distGPS-methods	distGPS
domainDist	domainDist
find.fdr	diffGenes
find.threshold	diffGenes
geneSetGPS	geneSetGPS
geneSetGPS,data.frame,mds,character-method	geneSetGPS
geneSetGPS,matrix,mds,character-method	geneSetGPS
geneSetGPS-methods	geneSetGPS
getPoints	mds
getPoints,mds-method	mds
getR2	mds
getR2,mds-method	mds
getStress	mds
getStress,mds-method	mds
getURL	getURL
gff2RDList	gff2RDList
gps2xgmml	gps2xgmml
gps2xgmml,mds,ANY-method	gps2xgmml
gps2xgmml,mds-method	gps2xgmml
hclust-class	clusGPS-class
is.adj	mds
is.adj,mds-method	mds
m.origs	s2
mds	mds
mds,distGPS,mds-method	mds-class
mds,distGPS,missing-method	mds
mds,splitDistGPS,missing-method	mds
mds-class	mds-class
mds-methods	mds
mergeClusters	mergeClusters
mergeClusters,clusGPS-method	mergeClusters
mergeClusters,list-method	mergeClusters
mergeClusters-methods	mergeClusters
mergeReplicateList	mergeReplicates
mergeReplicateMatrix	mergeReplicates
mergeReplicateMDS	mergeReplicates
mergeReplicates	mergeReplicates
mergeReplicates,data.frame-method	mergeReplicates
mergeReplicates,GRangesList-method	mergeReplicates
mergeReplicates,list-method	mergeReplicates
mergeReplicates,matrix-method	mergeReplicates
mergeReplicates,mds-method	mergeReplicates
mergeReplicates-methods	mergeReplicates
plot,clusGPS,ANY-method	clusGPS-class
plot,clusGPS-method	clusGPS-class
plot,mds,ANY-method	mds
plot,mds-method	mds-class
plotContour	clusGPS
plotDiffGenes	diffGenes
procrustesAdj	procrustesAdj
procrustesAdj,mds,distGPS-method	procrustesAdj
procrustesAdj-methods	procrustesAdj
profileClusters	profileClusters
rankFactorsbyDomain	rankFactorsbyDomain
rankFactorsbyDomain,data.frame-method	rankFactorsbyDomain
rankFactorsbyDomain,distGPS-method	rankFactorsbyDomain
rankFactorsbyDomain,matrix-method	rankFactorsbyDomain
rankFactorsbyDomain-methods	rankFactorsbyDomain
rankFactorsbyProfile	rankFactorsbyProfile
repliSeq	s2
s2	s2
s2.tab	s2
s2.wt	s2
s2names	s2
s2Seq	s2
s2SeqNames	s2
show,clusGPS-method	clusGPS-class
show,distGPS-method	distGPS-class
show,mds-method	mds-class
show,splitDistGPS-method	splitDistGPS-class
splidDistGPS-class	splitDistGPS-class
splitDistGPS,data.frame-method	distGPS
splitDistGPS,distGPS-method	splitDistGPS-class
splitDistGPS,matrix-method	distGPS
splitDistGPS-class	distGPS-class
tabClusters	clusGPS
tabClusters,clusGPS-method	clusGPS
toydists	s2
uniqueCount	distGPS
