gCMAP-package	gCMAP-package
.DESeq_nbinom	DESeq_nbinom
annotate_eset_list	annotate_eset_list
camera_score	camera_score-methods
camera_score,eSet,CMAPCollection-method	camera_score-methods
camera_score,eSet,GeneSet-method	camera_score-methods
camera_score,eSet,GeneSetCollection-method	camera_score-methods
camera_score,matrix,CMAPCollection-method	camera_score-methods
camera_score,matrix,GeneSet-method	camera_score-methods
camera_score,matrix,GeneSetCollection-method	camera_score-methods
camera_score-methods	camera_score-methods
center_eSet	center_eSet
CMAPCollection	CMAPCollection-class
CMAPCollection,environment-method	CMAPCollection-class
CMAPCollection,Matrix-method	CMAPCollection-class
CMAPCollection,matrix-method	CMAPCollection-class
CMAPCollection,missing-method	CMAPCollection-class
CMAPCollection-class	CMAPCollection-class
CMAPResults	CMAPResults-class
CMAPResults-class	CMAPResults-class
cmapTable	CMAPResults-class
cmapTable,CMAPResults-method	CMAPResults-class
connectivity_score	connectivity_score-methods
connectivity_score,ANY,GeneSet-method	connectivity_score-methods
connectivity_score,eSet,CMAPCollection-method	connectivity_score-methods
connectivity_score,eSet,GeneSetCollection-method	connectivity_score-methods
connectivity_score,eSet,SignedGeneSet-method	connectivity_score-methods
connectivity_score,matrix,CMAPCollection-method	connectivity_score-methods
connectivity_score,matrix,GeneSetCollection-method	connectivity_score-methods
connectivity_score,matrix,SignedGeneSet-method	connectivity_score-methods
docs	CMAPResults-class
docs,CMAPResults-method	CMAPResults-class
docs<-	CMAPResults-class
docs<-,CMAPResults-method	CMAPResults-class
downIds	SignedGeneSet-class
downIds,CMAPCollection-method	CMAPCollection-class
downIds,SignedGeneSet-method	SignedGeneSet-class
effect	CMAPResults-class
effect,CMAPResults-method	CMAPResults-class
effect<-	CMAPResults-class
effect<-,CMAPResults-method	CMAPResults-class
errors	CMAPResults-class
errors,CMAPResults-method	CMAPResults-class
errors<-	CMAPResults-class
errors<-,CMAPResults-method	CMAPResults-class
eSetOnDisk	eSetOnDisk
eset_instances	eset_instances
featureScores	featureScores-methods
featureScores,BigMatrix,CMAPCollection-method	featureScores-methods
featureScores,CMAPCollection,BigMatrix-method	featureScores-methods
featureScores,CMAPCollection,CMAPCollection-method	featureScores-methods
featureScores,CMAPCollection,eSet-method	featureScores-methods
featureScores,CMAPCollection,matrix-method	featureScores-methods
featureScores,CMAPCollection,matrix_or_big.matrix-method	featureScores-methods
featureScores,CMAPCollection,numeric-method	featureScores-methods
featureScores,eSet,CMAPCollection-method	featureScores-methods
featureScores,matrix,CMAPCollection-method	featureScores-methods
featureScores,matrix_or_big.matrix,CMAPCollection-method	featureScores-methods
featureScores,numeric,CMAPCollection-method	featureScores-methods
featureScores-methods	featureScores-methods
fisher_score	fisher_score-methods
fisher_score,CMAPCollection,CMAPCollection,character-method	fisher_score-methods
fisher_score,CMAPCollection,GeneSetCollection,character-method	fisher_score-methods
fisher_score,CMAPCollection,NChannelSet,character-method	fisher_score-methods
fisher_score,GeneSet,CMAPCollection,character-method	fisher_score-methods
fisher_score,GeneSet,GeneSet,character-method	fisher_score-methods
fisher_score,GeneSet,GeneSetCollection,character-method	fisher_score-methods
fisher_score,GeneSet,NChannelSet,character-method	fisher_score-methods
fisher_score,GeneSetCollection,CMAPCollection,character-method	fisher_score-methods
fisher_score,GeneSetCollection,GeneSetCollection,character-method	fisher_score-methods
fisher_score,GeneSetCollection,NChannelSet,character-method	fisher_score-methods
fisher_score,SignedGeneSet,CMAPCollection,character-method	fisher_score-methods
fisher_score,SignedGeneSet,NChannelSet,character-method	fisher_score-methods
fisher_score-methods	fisher_score-methods
gCMAP	gCMAP-package
gCMAPData	gCMAPData-dataset
GeneColorSet,NChannelSet-method	GeneSet-methods
geneIds,CMAPCollection-method	CMAPCollection-class
geneIndex	geneIndex-methods
geneIndex,CMAPCollection,character-method	geneIndex-methods
geneIndex,GeneSet,character-method	geneIndex-methods
geneIndex,GeneSetCollection,character-method	geneIndex-methods
geneIndex-methods	geneIndex-methods
generate_gCMAP_NChannelSet	generate_gCMAP_NChannelSet
geneScores	CMAPResults-class
geneScores,CMAPResults-method	CMAPResults-class
GeneSet	GeneSet-methods
GeneSet,NChannelSet-method	GeneSet-methods
geneSign	SignedGeneSet-class
geneSign,SignedGeneSet-method	SignedGeneSet-class
geneSign<-	SignedGeneSet-class
geneSign<-,SignedGeneSet,character-method	SignedGeneSet-class
geneSign<-,SignedGeneSet,factor-method	SignedGeneSet-class
go2cmap	KEGG2cmap
gsealm_jg_score	gsealm_jg_score-methods
gsealm_jg_score,CMAPCollection,eSet-method	gsealm_jg_score-methods
gsealm_jg_score,CMAPCollection,matrix-method	gsealm_jg_score-methods
gsealm_jg_score,CMAPCollection,numeric-method	gsealm_jg_score-methods
gsealm_jg_score,eSet,CMAPCollection-method	gsealm_jg_score-methods
gsealm_jg_score,eSet,GeneSet-method	gsealm_jg_score-methods
gsealm_jg_score,eSet,GeneSetCollection-method	gsealm_jg_score-methods
gsealm_jg_score,GeneSet,eSet-method	gsealm_jg_score-methods
gsealm_jg_score,GeneSet,matrix-method	gsealm_jg_score-methods
gsealm_jg_score,GeneSet,numeric-method	gsealm_jg_score-methods
gsealm_jg_score,GeneSetCollection,eSet-method	gsealm_jg_score-methods
gsealm_jg_score,GeneSetCollection,matrix-method	gsealm_jg_score-methods
gsealm_jg_score,GeneSetCollection,numeric-method	gsealm_jg_score-methods
gsealm_jg_score,matrix,GeneSet-method	gsealm_jg_score-methods
gsealm_jg_score,matrix,GeneSetCollection-method	gsealm_jg_score-methods
gsealm_jg_score,matrix_or_big.matrix,CMAPCollection-method	gsealm_jg_score-methods
gsealm_jg_score,numeric,CMAPCollection-method	gsealm_jg_score-methods
gsealm_jg_score,numeric,GeneSet-method	gsealm_jg_score-methods
gsealm_jg_score,numeric,GeneSetCollection-method	gsealm_jg_score-methods
gsealm_jg_score-methods	gsealm_jg_score-methods
gsealm_score	gsealm_score-methods
gsealm_score,eSet,CMAPCollection-method	gsealm_score-methods
gsealm_score,eSet,GeneSet-method	gsealm_score-methods
gsealm_score,eSet,GeneSetCollection-method	gsealm_score-methods
gsealm_score,ExpressionSet,CMAPCollection-method	gsealm_score-methods
gsealm_score,ExpressionSet,GeneSet-method	gsealm_score-methods
gsealm_score,ExpressionSet,GeneSetCollection-method	gsealm_score-methods
gsealm_score,matrix,CMAPCollection-method	gsealm_score-methods
gsealm_score,matrix,GeneSet-method	gsealm_score-methods
gsealm_score,matrix,GeneSetCollection-method	gsealm_score-methods
gsealm_score-methods	gsealm_score-methods
incidence,CMAPCollection-method	CMAPCollection-class
incidence,GeneSetCollection-method	SignedGeneSet-class
incidence,list-method	CMAPCollection-class
incidence,SignedGeneSet-method	SignedGeneSet-class
induceCMAPCollection	induceCMAPCollection-methods
induceCMAPCollection,eSet-method	induceCMAPCollection-methods
induceCMAPCollection,matrix-method	induceCMAPCollection-methods
induceCMAPCollection-methods	induceCMAPCollection-methods
initialize,CMAPCollection-method	CMAPCollection-class
initialize,CMAPResults-method	CMAPResults-class
initialize,SignedGeneSet-method	SignedGeneSet-class
KEGG2cmap	KEGG2cmap
ks	connectivity_score-methods
labels	CMAPResults-class
labels,CMAPResults-method	CMAPResults-class
labels<-	CMAPResults-class
labels<-,CMAPResults-method	CMAPResults-class
mapIdentifiers,SignedGeneSet,GeneIdentifierType,GeneIdentifierType-method	SignedGeneSet-class
mapIdentifiers,SignedGeneSet,GeneIdentifierType,missing-method	SignedGeneSet-class
mapIdentifiers,SignedGeneSet,missing,ANY-method	SignedGeneSet-class
mapNmerge	mapNmerge
matrix_or_big.matrix-class	matrix_or_big.matrix-class
members	CMAPCollection-class
members,CMAPCollection-method	CMAPCollection-class
memorize	memorize
mergeCMAPs	mergeCMAPs
mergeCollections	CMAPCollection-class
mergeCollections,CMAPCollection,CMAPCollection-method	CMAPCollection-class
mgsa_score	mgsa_score-methods
mgsa_score,CMAPCollection,CMAPCollection,character-method	mgsa_score-methods
mgsa_score,CMAPCollection,GeneSetCollection,character-method	mgsa_score-methods
mgsa_score,GeneSet,CMAPCollection,character-method	mgsa_score-methods
mgsa_score,GeneSet,GeneSet,character-method	mgsa_score-methods
mgsa_score,GeneSet,GeneSetCollection,character-method	mgsa_score-methods
mgsa_score,GeneSet,NChannelSet,character-method	mgsa_score-methods
mgsa_score,GeneSetCollection,CMAPCollection,character-method	mgsa_score-methods
mgsa_score,GeneSetCollection,GeneSetCollection,character-method	mgsa_score-methods
mgsa_score,GeneSetCollection,NChannelSet,character-method	mgsa_score-methods
mgsa_score,SignedGeneSet,CMAPCollection,character-method	mgsa_score-methods
mgsa_score,SignedGeneSet,NChannelSet,character-method	mgsa_score-methods
mgsa_score-methods	mgsa_score-methods
minSetSize	minSetSize-methods
minSetSize,CMAPCollection-method	minSetSize-methods
mroast_score	mroast_score-methods
mroast_score,eSet,CMAPCollection-method	mroast_score-methods
mroast_score,eSet,GeneSet-method	mroast_score-methods
mroast_score,eSet,GeneSetCollection-method	mroast_score-methods
mroast_score,matrix,CMAPCollection-method	mroast_score-methods
mroast_score,matrix,GeneSet-method	mroast_score-methods
mroast_score,matrix,GeneSetCollection-method	mroast_score-methods
mroast_score-methods	mroast_score-methods
nFound	CMAPResults-class
nFound,CMAPResults-method	CMAPResults-class
nFound<-	CMAPResults-class
nFound<-,CMAPResults-method	CMAPResults-class
nSet	CMAPResults-class
nSet,CMAPResults-method	CMAPResults-class
nSet<-	CMAPResults-class
nSet<-,CMAPResults-method	CMAPResults-class
padj	CMAPResults-class
padj,CMAPResults-method	CMAPResults-class
padj<-	CMAPResults-class
padj<-,CMAPResults-method	CMAPResults-class
pairwise_compare	pairwise_compare
pairwise_compare_limma	pairwise_compare
pairwise_DESeq	pairwise_DESeq
plot,CMAPResults,ANY-method	CMAPResults-class
pval	CMAPResults-class
pval,CMAPResults-method	CMAPResults-class
pval<-	CMAPResults-class
pval<-,CMAPResults-method	CMAPResults-class
reactome2cmap	KEGG2cmap
romer_score	romer_score-methods
romer_score,eSet,CMAPCollection-method	romer_score-methods
romer_score,eSet,GeneSet-method	romer_score-methods
romer_score,eSet,GeneSetCollection-method	romer_score-methods
romer_score,matrix,CMAPCollection-method	romer_score-methods
romer_score,matrix,GeneSet-method	romer_score-methods
romer_score,matrix,GeneSetCollection-method	romer_score-methods
romer_score-methods	romer_score-methods
S	connectivity_score-methods
s	connectivity_score-methods
set	CMAPResults-class
set,CMAPResults-method	CMAPResults-class
set<-	CMAPResults-class
set<-,CMAPResults-method	CMAPResults-class
setSizes	CMAPCollection-class
setSizes,CMAPCollection-method	CMAPCollection-class
show,CMAPResults-method	CMAPResults-class
show,SignedGeneSet-method	SignedGeneSet-class
signed	CMAPCollection-class
signed,CMAPCollection-method	CMAPCollection-class
signed<-	CMAPCollection-class
signed<-,CMAPCollection-method	CMAPCollection-class
SignedGeneSet	SignedGeneSet-methods
SignedGeneSet,ANY-method	SignedGeneSet-methods
SignedGeneSet,missing-method	SignedGeneSet-methods
SignedGeneSet-class	SignedGeneSet-class
signedRankSumTest	signedRankSumTest
splitPerturbations	splitPerturbations
trend	CMAPResults-class
trend,CMAPResults-method	CMAPResults-class
trend<-	CMAPResults-class
trend<-,CMAPResults-method	CMAPResults-class
upIds	SignedGeneSet-class
upIds,CMAPCollection-method	CMAPCollection-class
upIds,SignedGeneSet-method	SignedGeneSet-class
wiki2cmap	KEGG2cmap
wilcox_score	wilcox_score-methods
wilcox_score,CMAPCollection,eSet-method	wilcox_score-methods
wilcox_score,CMAPCollection,matrix-method	wilcox_score-methods
wilcox_score,CMAPCollection,numeric-method	wilcox_score-methods
wilcox_score,eSet,CMAPCollection-method	wilcox_score-methods
wilcox_score,eSet,GeneSet-method	wilcox_score-methods
wilcox_score,eSet,GeneSetCollection-method	wilcox_score-methods
wilcox_score,GeneSet,eSet-method	wilcox_score-methods
wilcox_score,GeneSet,matrix-method	wilcox_score-methods
wilcox_score,GeneSet,numeric-method	wilcox_score-methods
wilcox_score,GeneSetCollection,eSet-method	wilcox_score-methods
wilcox_score,GeneSetCollection,matrix-method	wilcox_score-methods
wilcox_score,GeneSetCollection,numeric-method	wilcox_score-methods
wilcox_score,matrix,CMAPCollection-method	wilcox_score-methods
wilcox_score,matrix,GeneSet-method	wilcox_score-methods
wilcox_score,matrix,GeneSetCollection-method	wilcox_score-methods
wilcox_score,numeric,CMAPCollection-method	wilcox_score-methods
wilcox_score,numeric,GeneSet-method	wilcox_score-methods
wilcox_score,numeric,GeneSetCollection-method	wilcox_score-methods
wilcox_score-methods	wilcox_score-methods
zScores	zScores
zscores	CMAPResults-class
zscores,CMAPResults-method	CMAPResults-class
