BulkSignalR-package	BulkSignalR-package
.buildPermutatedCountMatrix	dot-buildPermutatedCountMatrix
.buildPermutationIndices	dot-buildPermutationIndices
.cacheAdd	dot-cacheAdd
.cacheCheckIn	dot-cacheCheckIn
.cdfAlphaStable	dot-cdfAlphaStable
.cdfEmpirical	dot-cdfEmpirical
.cdfGaussian	dot-cdfGaussian
.cdfKernelEmpirical	dot-cdfKernelEmpirical
.cdfMixedGaussian	dot-cdfMixedGaussian
.checkInteroperabilityForCounts	dot-checkInteroperabilityForCounts
.checkRDSFromCache	dot-checkRDSFromCache
.checkReceptorSignaling	dot-checkReceptorSignaling
.checkRegulatedReceptorSignaling	dot-checkRegulatedReceptorSignaling
.customheatmap	dot-customheatmap
.cutExtremeValues	dot-cutExtremeValues
.downstreamRegulatedSignaling	dot-downstreamRegulatedSignaling
.downstreamSignaling	dot-downstreamSignaling
.edgesLRIntracell	dot-edgesLRIntracell
.formatPathwaysFromGmt	dot-formatPathwaysFromGmt
.formatPathwaysFromJson	dot-formatPathwaysFromJson
.formatPathwaysFromTxt	dot-formatPathwaysFromTxt
.geneNameConversion	dot-geneNameConversion
.getAlphaStableParam	dot-getAlphaStableParam
.getCorrelatedLR	dot-getCorrelatedLR
.getEmpiricalNull	dot-getEmpiricalNull
.getEmpiricalNullCorrLR	dot-getEmpiricalNullCorrLR
.getEmpiricalParam	dot-getEmpiricalParam
.getGaussianParam	dot-getGaussianParam
.getKernelEmpiricalParam	dot-getKernelEmpiricalParam
.getMixedGaussianParam	dot-getMixedGaussianParam
.getRegulatedLR	dot-getRegulatedLR
.pValuesLR	dot-pValuesLR
.pValuesRegulatedLR	dot-pValuesRegulatedLR
.readRDSFromCache	dot-readRDSFromCache
.shufflePermutationIndices	dot-shufflePermutationIndices
.testCacheFiles	dot-testCacheFiles
.testRemoteServer	dot-testRemoteServer
addClusterComp	addClusterComp
addClusterComp,BSRDataModelComp-method	addClusterComp
alluvialPlot	alluvialPlot
annotation.spa	annotation.spa
assignCellTypesToInteractions	assignCellTypesToInteractions
bodyMap.mouse	bodyMap.mouse
BSRClusterComp	BSRClusterComp
BSRClusterComp-class	BSRClusterComp-class
BSRDataModel	BSRDataModel
BSRDataModel-class	BSRDataModel-class
BSRDataModelComp	BSRDataModelComp
BSRDataModelComp-class	BSRDataModelComp-class
bsrdm	bsrdm
bsrdm.comp	bsrdm.comp
bsrdm.spa	bsrdm.spa
bsrinf	bsrinf
bsrinf.comp	bsrinf.comp
bsrinf.mouse	bsrinf.mouse
bsrinf.spa	bsrinf.spa
BSRInference	BSRInference
BSRInference-class	BSRInference-class
BSRInferenceComp	BSRInferenceComp
BSRInferenceComp-class	BSRInferenceComp-class
BSRSignature	BSRSignature
BSRSignature-class	BSRSignature-class
BSRSignatureComp	BSRSignatureComp
BSRSignatureComp-class	BSRSignatureComp-class
bubblePlotPathwaysLR	bubblePlotPathwaysLR
BulkSignalR	BulkSignalR-package
cacheClear	cacheClear
cacheInfo	cacheInfo
cacheVersion	cacheVersion
cellTypeFrequency	cellTypeFrequency
cellularNetwork	cellularNetwork
cellularNetworkTable	cellularNetworkTable
chordDiagramLR	chordDiagramLR
coerce	coerce
coerce,BSRDataModel,BSRDataModelComp-method	coerce
colClusterA	colClusterA
colClusterA,BSRClusterComp-method	colClusterA
colClusterA<-,BSRClusterComp-method	colClusterA-set-BSRClusterComp-method
colClusterB	colClusterB
colClusterB,BSRClusterComp-method	colClusterB
colClusterB<-,BSRClusterComp-method	colClusterB-set-BSRClusterComp-method
comparison	comparison
comparison,BSRDataModelComp-method	comparison
comparison<-,BSRDataModelComp-method	comparison-set-BSRDataModelComp-method
comparisonName	comparisonName
comparisonName,BSRInferenceComp-method	comparisonName
comparisonName,BSRSignatureComp-method	comparisonName
comparisonName<-,BSRInferenceComp-method	comparisonName-set-BSRInferenceComp-method
convertToHuman	convertToHuman
createResources	createResources
differentialStats	differentialStats
differentialStats,BSRClusterComp-method	differentialStats
differentialStats<-,BSRClusterComp-method	differentialStats-set-BSRClusterComp-method
findOrthoGenes	findOrthoGenes
generateSpatialPlots	generateSpatialPlots
getLRIntracellNetwork	getLRIntracellNetwork
getLRNetwork	getLRNetwork
getPathwayStats	getPathwayStats
getPathwayStats,BSRInference-method	getPathwayStats
getResource	getResource
immune.signatures	immune.signatures
inferenceParameters	inferenceParameters
inferenceParameters,BSRInference-method	inferenceParameters
inferenceParameters<-,BSRInference-method	inferenceParameters-set-BSRInference-method
initialOrganism	initialOrganism
initialOrganism,BSRDataModel-method	initialOrganism
initialOrthologs	initialOrthologs
initialOrthologs,BSRDataModel-method	initialOrthologs
learnParameters	learnParameters
learnParameters,BSRDataModel-method	learnParameters
ligands	ligands
ligands,BSRInference-method	ligands
ligands,BSRSignature-method	ligands
ligands<-,BSRInference-method	ligands-set-BSRInference-method
logTransformed	logTransformed
logTransformed,BSRDataModel-method	logTransformed
LRinter	LRinter
LRinter,BSRInference-method	LRinter
LRinter<-,BSRInference-method	LRinter-set-BSRInference-method
LRinterScore	LRinterScore
LRinterScore,BSRInferenceComp-method	LRinterScore
LRinterShort	LRinterShort
LRinterShort,BSRInference-method	LRinterShort
LRinterShort,BSRInferenceComp-method	LRinterShort
maxLigandSpatialCounts	maxLigandSpatialCounts
mu	mu
mu,BSRDataModelComp-method	mu
mu<-,BSRDataModelComp-method	mu-set-BSRDataModelComp-method
ncounts	ncounts
ncounts,BSRDataModel-method	ncounts
ncounts<-,BSRDataModel-method	ncounts-set-BSRDataModel-method
normalization	normalization
normalization,BSRDataModel-method	normalization
ortholog.dict	ortholog.dict
p.EMT	p.EMT
parameters	parameters
parameters,BSRDataModel-method	parameters
parameters<-,BSRDataModel-method	parameters-set-BSRDataModel-method
pathways	pathways
pathways,BSRSignature-method	pathways
receptors	receptors
receptors,BSRInference-method	receptors
receptors,BSRSignature-method	receptors
receptors<-,BSRInference-method	receptors-set-BSRInference-method
reduceToBestPathway	reduceToBestPathway
reduceToBestPathway,BSRInference-method	reduceToBestPathway
reduceToBestPathway,BSRInferenceComp-method	reduceToBestPathway
reduceToLigand	reduceToLigand
reduceToLigand,BSRInference-method	reduceToLigand
reduceToLigand,BSRInferenceComp-method	reduceToLigand
reduceToPathway	reduceToPathway
reduceToPathway,BSRInference-method	reduceToPathway
reduceToPathway,BSRInferenceComp-method	reduceToPathway
reduceToReceptor	reduceToReceptor
reduceToReceptor,BSRInference-method	reduceToReceptor
reduceToReceptor,BSRInferenceComp-method	reduceToReceptor
relateToGeneSet	relateToGeneSet
removeClusterComp	removeClusterComp
removeClusterComp,BSRDataModelComp-method	removeClusterComp
rescoreInference	rescoreInference
rescoreInference,BSRInference-method	rescoreInference
rescoreInference,BSRInferenceComp-method	rescoreInference
resetLRdb	resetLRdb
resetNetwork	resetNetwork
resetPathways	resetPathways
resetToInitialOrganism	resetToInitialOrganism
resetToInitialOrganism,BSRInference-method	resetToInitialOrganism
scoreLRGeneSignatures	scoreLRGeneSignatures
scoreLRGeneSignatures,BSRDataModel-method	scoreLRGeneSignatures
scoreLRGeneSignatures,BSRDataModelComp-method	scoreLRGeneSignatures
scoreSignatures	scoreSignatures
sdc	sdc
separatedLRPlot	separatedLRPlot
signatureHeatmaps	signatureHeatmaps
simpleHeatmap	simpleHeatmap
smoothSpatialCounts	smoothSpatialCounts
sourceComparisonName	sourceComparisonName
sourceComparisonName,BSRInferenceComp-method	sourceComparisonName
sourceComparisonName<-,BSRInferenceComp-method	sourceComparisonName-set-BSRInferenceComp-method
spatialAssociation	spatialAssociation
spatialAssociationPlot	spatialAssociationPlot
spatialDiversityPlot	spatialDiversityPlot
spatialIndexPlot	spatialIndexPlot
spatialPlot	spatialPlot
summarizedCellularNetwork	summarizedCellularNetwork
tgCorr	tgCorr
tgCorr,BSRInference-method	tgCorr
tgCorr,BSRSignature-method	tgCorr
tgCorr<-,BSRInference-method	tgCorr-set-BSRInference-method
tgExpr	tgExpr
tgExpr,BSRInferenceComp-method	tgExpr
tgExpr,BSRSignatureComp-method	tgExpr
tgExpr<-,BSRInferenceComp-method	tgExpr-set-BSRInferenceComp-method
tgGenes	tgGenes
tgGenes,BSRInference-method	tgGenes
tgGenes,BSRSignature-method	tgGenes
tgGenes<-,BSRInference-method	tgGenes-set-BSRInference-method
tgLogFC	tgLogFC
tgLogFC,BSRInferenceComp-method	tgLogFC
tgLogFC,BSRSignatureComp-method	tgLogFC
tgLogFC<-,BSRInferenceComp-method	tgLogFC-set-BSRInferenceComp-method
tgPval	tgPval
tgPval,BSRInferenceComp-method	tgPval
tgPval,BSRSignatureComp-method	tgPval
tgPval<-,BSRInferenceComp-method	tgPval-set-BSRInferenceComp-method
tme.signatures	tme.signatures
updateInference	updateInference
updateInference,BSRInferenceComp-method	updateInference
