AdjData	AdjData-class
AdjData-class	AdjData-class
adjMatrix	Onto-method
adjMatrix,Cnetwork-method	Cnetwork-method
adjMatrix,Dnetwork-method	Dnetwork-method
adjMatrix,Onto-method	Onto-method
adjp	Eoutput-method
adjp,Coutput-method	Coutput-method
adjp,Eoutput-method	Eoutput-method
Ancestral_domainome	Ancestral_domainome
Anno	Anno-class
Anno-class	Anno-class
Anno-method	Anno-method
AnnoData	AnnoData-class
annoData	Anno-method
annoData,Anno-method	Anno-method
AnnoData-class	AnnoData-class
Cnetwork	Cnetwork-class
cnetwork	Coutput-method
cnetwork,Coutput-method	Coutput-method
Cnetwork-class	Cnetwork-class
Cnetwork-method	Cnetwork-method
colNames	InfoDataFrame-method
colNames,InfoDataFrame-method	InfoDataFrame-method
Coutput	Coutput-class
Coutput-class	Coutput-class
Coutput-method	Coutput-method
Data	InfoDataFrame-method
Data,InfoDataFrame-method	InfoDataFrame-method
data.frame2InfoDataFrame	InfoDataFrame-method
dcAlgo	dcAlgo
dcAlgoPredict	dcAlgoPredict
dcAlgoPredictGenome	dcAlgoPredictGenome
dcAlgoPredictMain	dcAlgoPredictMain
dcAlgoPredictPR	dcAlgoPredictPR
dcAlgoPropagate	dcAlgoPropagate
dcAncestralML	dcAncestralML
dcAncestralMP	dcAncestralMP
dcBuildAnno	dcBuildAnno
dcBuildInfoDataFrame	dcBuildInfoDataFrame
dcBuildOnto	dcBuildOnto
dcConverter	dcConverter
dcDAGannotate	dcDAGannotate
dcDAGdomainSim	dcDAGdomainSim
dcDuplicated	dcDuplicated
dcEnrichment	dcEnrichment
dcFunArgs	dcFunArgs
dcList2Matrix	dcList2Matrix
dcNaivePredict	dcNaivePredict
dcRDataLoader	dcRDataLoader
dcRWRpipeline	dcRWRpipeline
dcRWRpredict	dcRWRpredict
dcSparseMatrix	dcSparseMatrix
dcSplitArch	dcSplitArch
dcSubtreeClade	dcSubtreeClade
dcSubtreeTips	dcSubtreeTips
dcSupraBetter	dcSupraBetter
dcTreeConnectivity	dcTreeConnectivity
dData	Anno-method
dData,Anno-method	Anno-method
description	Dnetwork-method
description,Dnetwork-method	Dnetwork-method
dgCMatrix2Anno	Anno-method
dgCMatrix2Cnetwork	Cnetwork-method
dgCMatrix2Dnetwork	Dnetwork-method
dgCMatrix2Onto	Onto-method
dim,Anno-method	Anno-method
dim,Cnetwork-method	Cnetwork-method
dim,Dnetwork-method	Dnetwork-method
dim,InfoDataFrame-method	InfoDataFrame-method
dim,Onto-method	Onto-method
dimLabels	InfoDataFrame-method
dimLabels,InfoDataFrame-method	InfoDataFrame-method
Dnetwork	Dnetwork-class
Dnetwork-class	Dnetwork-class
Dnetwork-method	Dnetwork-method
domainData	Anno-method
domainData,Anno-method	Anno-method
domainNames	Anno-method
domainNames,Anno-method	Anno-method
Eoutput	Eoutput-class
Eoutput-class	Eoutput-class
Eoutput-method	Eoutput-method
eTOL	eTOL
id	Dnetwork-method
id,Dnetwork-method	Dnetwork-method
InfoDataFrame	InfoDataFrame-class
InfoDataFrame-class	InfoDataFrame-class
InfoDataFrame-method	InfoDataFrame-method
InterPro	InterPro
InterPro2GOBP	InterPro2GOBP
InterPro2GOCC	InterPro2GOCC
InterPro2GOMF	InterPro2GOMF
level	Dnetwork-method
level,Dnetwork-method	Dnetwork-method
matrix2Anno	Anno-method
matrix2Cnetwork	Cnetwork-method
matrix2Dnetwork	Dnetwork-method
matrix2Onto	Onto-method
ncol	InfoDataFrame-method
ncol,InfoDataFrame-method	InfoDataFrame-method
nInfo	Onto-method
nInfo,Cnetwork-method	Cnetwork-method
nInfo,Dnetwork-method	Dnetwork-method
nInfo,Onto-method	Onto-method
nodeInfo	Onto-method
nodeInfo,Cnetwork-method	Cnetwork-method
nodeInfo,Dnetwork-method	Dnetwork-method
nodeInfo,Onto-method	Onto-method
nodeNames	Onto-method
nodeNames,Cnetwork-method	Cnetwork-method
nodeNames,Dnetwork-method	Dnetwork-method
nodeNames,Onto-method	Onto-method
nrow	InfoDataFrame-method
nrow,InfoDataFrame-method	InfoDataFrame-method
Onto	Onto-class
Onto-class	Onto-class
Onto-method	Onto-method
onto.DO	onto.DO
onto.GOBP	onto.GOBP
onto.GOCC	onto.GOCC
onto.GOMF	onto.GOMF
onto.HPMI	onto.HPMI
onto.HPON	onto.HPON
onto.HPPA	onto.HPPA
onto.MP	onto.MP
Pfam	Pfam
Pfam2GOBP	Pfam2GOBP
Pfam2GOCC	Pfam2GOCC
Pfam2GOMF	Pfam2GOMF
pvalue	Eoutput-method
pvalue,Coutput-method	Coutput-method
pvalue,Eoutput-method	Eoutput-method
ratio	Coutput-method
ratio,Coutput-method	Coutput-method
Rfam	Rfam
Rfam2GOBP	Rfam2GOBP
Rfam2GOCC	Rfam2GOCC
Rfam2GOMF	Rfam2GOMF
rowNames	InfoDataFrame-method
rowNames,InfoDataFrame-method	InfoDataFrame-method
SCOP.fa	SCOP.fa
SCOP.fa2DO	SCOP.fa2DO
SCOP.fa2GOBP	SCOP.fa2GOBP
SCOP.fa2GOCC	SCOP.fa2GOCC
SCOP.fa2GOMF	SCOP.fa2GOMF
SCOP.fa2HPMI	SCOP.fa2HPMI
SCOP.fa2HPON	SCOP.fa2HPON
SCOP.fa2HPPA	SCOP.fa2HPPA
SCOP.fa2MP	SCOP.fa2MP
SCOP.sf	SCOP.sf
SCOP.sf2DO	SCOP.sf2DO
SCOP.sf2GOBP	SCOP.sf2GOBP
SCOP.sf2GOCC	SCOP.sf2GOCC
SCOP.sf2GOMF	SCOP.sf2GOMF
SCOP.sf2HPMI	SCOP.sf2HPMI
SCOP.sf2HPON	SCOP.sf2HPON
SCOP.sf2HPPA	SCOP.sf2HPPA
SCOP.sf2MP	SCOP.sf2MP
show,Anno-method	Anno-method
show,Cnetwork-method	Cnetwork-method
show,Coutput-method	Coutput-method
show,Dnetwork-method	Dnetwork-method
show,Eoutput-method	Eoutput-method
show,InfoDataFrame-method	InfoDataFrame-method
show,Onto-method	Onto-method
tData	Anno-method
tData,Anno-method	Anno-method
termData	Anno-method
termData,Anno-method	Anno-method
termNames	Anno-method
termNames,Anno-method	Anno-method
term_distance	Onto-method
term_distance,Onto-method	Onto-method
term_id	Onto-method
term_id,Onto-method	Onto-method
term_name	Onto-method
term_name,Onto-method	Onto-method
term_namespace	Onto-method
term_namespace,Onto-method	Onto-method
view	Eoutput-method
view,Eoutput-method	Eoutput-method
visEnrichment	visEnrichment
write	Eoutput-method
write,Coutput-method	Coutput-method
write,Eoutput-method	Eoutput-method
zscore	Eoutput-method
zscore,Coutput-method	Coutput-method
zscore,Eoutput-method	Eoutput-method
[,Anno,ANY,ANY,ANY-method	Anno-method
[,Anno-method	Anno-method
[,Cnetwork,ANY,ANY,ANY-method	Cnetwork-method
[,Cnetwork-method	Cnetwork-method
[,Dnetwork,ANY,ANY,ANY-method	Dnetwork-method
[,Dnetwork-method	Dnetwork-method
[,InfoDataFrame,ANY,ANY,ANY-method	InfoDataFrame-method
[,InfoDataFrame-method	InfoDataFrame-method
[,Onto,ANY,ANY,ANY-method	Onto-method
[,Onto-method	Onto-method
