VISION-package	VISION
.colNormHelper	dot-colNormHelper
addLatentSpace	addLatentSpace
addProjection	addProjection-Vision-method
addProjection,Vision-method	addProjection-Vision-method
addSignatures	addSignatures
addTSNE	addTSNE
addUMAP	addUMAP
analyze	analyze-Vision-method
analyze,Vision-method	analyze-Vision-method
analyzeLocalCorrelations	analyzeLocalCorrelations
analyzeTrajectoryCorrelations	analyzeTrajectoryCorrelations
annotateLatentComponents	annotateLatentComponents
applyFilters	applyFilters
applyICA	applyICA
applyISOMap	applyISOMap
applyMicroClustering	applyMicroClustering
applyPCA	applyPCA
applyPermutationWPCA	applyPermutationWPCA
applyRBFPCA	applyRBFPCA
applySimplePPT	applySimplePPT
applySpectralEmbedding	applySpectralEmbedding
applytSNE10	applytSNE10
applytSNE30	applytSNE30
applyUMAP	applyUMAP
batchify	batchify
batchSigEvalNorm	batchSigEvalNorm
calcInterEdgeDistMat	calcInterEdgeDistMat
calcIntraEdgeDistMat	calcIntraEdgeDistMat
calcSignatureScores	calcSignatureScores
calculateTrajectoryDistances	calculateTrajectoryDistances
clipBottom	clipBottom
Cluster	Cluster
clusterCells	clusterCells
clusterSignatures	clusterSignatures
clusterSigScores	clusterSigScores
colNormalization	colNormalization
colRankNormalization	colRankNormalization
colVarsSp	colVarsSp
computeKNNWeights,matrix-method	computeKNNWeights-matrix-method
computeKNNWeights,Trajectory-method	computeKNNWeights-Trajectory-method
computeLatentSpace	computeLatentSpace
computeProjectionGenes	computeProjectionGenes
convertGeneIds	convertGeneIds
coordinatesToJSON	coordinatesToJSON
createGeneSignature	createGeneSignature
createTrajectoryMetaData	createTrajectoryMetaData
evalSigGeneImportance	evalSigGeneImportance
evalSigGeneImportanceSparse	evalSigGeneImportanceSparse
fbConsistencyScores	fbConsistencyScores
filterGenesFano	filterGenesFano
filterGenesNovar	filterGenesNovar
filterGenesThreshold	filterGenesThreshold
find_knn_parallel	find_knn_parallel
fitTree	fitTree
geary_sig_v_proj	geary_sig_v_proj
generatePermutationNull	generatePermutationNull
generateProjections	generateProjections
generateProjectionsInner	generateProjectionsInner
generateTrajectoryProjections	generateTrajectoryProjections
getLatentSpace	getLatentSpace
getLatentSpace,Vision-method	getLatentSpace
getLatentTrajectory	getLatentTrajectory
getLatentTrajectory,Vision-method	getLatentTrajectory
getMetaAutocorrelation	getMetaAutocorrelation
getMetaAutocorrelation,Vision-method	getMetaAutocorrelation
getMetaDifferential	getMetaDifferential
getMetaDifferential,Vision-method	getMetaDifferential
getMSE	getMSE
getNormalizedCopy	getNormalizedCopy
getNormalizedCopySparse	getNormalizedCopySparse
getParam	getParam
getProjections	getProjections
getProjections,Vision-method	getProjections
getSelections	getSelections
getSelections,Vision-method	getSelections
getSignatureAutocorrelation	getSignatureAutocorrelation
getSignatureAutocorrelation,Vision-method	getSignatureAutocorrelation
getSignatureDifferential	getSignatureDifferential
getSignatureDifferential,Vision-method	getSignatureDifferential
getSignatureScores	getSignatureScores
getSignatureScores,Vision-method	getSignatureScores
hasUnnormalizedData	hasUnnormalizedData
ilog1p	ilog1p
innerEvalSignatureBatchNorm	innerEvalSignatureBatchNorm
launchServer	launchServer
louvainCluster	louvainCluster
matLog2	matLog2
matrix_chisq	matrix_chisq
matrix_wilcox	matrix_wilcox
matrix_wilcox_cpp	matrix_wilcox_cpp
noNormalization	noNormalization
NormData	NormData
pearsonCorrToJSON	pearsonCorrToJSON
poolCells	poolCells
poolMatrixCols	poolMatrixCols
poolMatrixCols_Inner	poolMatrixCols_Inner
poolMatrixRows	poolMatrixRows
poolMetaData	poolMetaData
processSignatures	processSignatures
projectOnTree	projectOnTree
readjust_clusters	readjust_clusters
readSignaturesInput	readSignaturesInput
read_10x	read_10x
read_10x_h5	read_10x_h5
read_10x_h5_v2	read_10x_h5_v2
read_10x_h5_v3	read_10x_h5_v3
registerMethods	registerMethods
rowAndColNormalization	rowAndColNormalization
rowNormalization	rowNormalization
rowVarsSp	rowVarsSp
saveAndViewResults	saveAndViewResults-Vision-method
saveAndViewResults,Vision-method	saveAndViewResults-Vision-method
ServerExpression	ServerExpression
ServerSigProjMatrix	ServerSigProjMatrix
sigConsistencyScores	sigConsistencyScores
Signature	Signature
signatureToJSON	signatureToJSON
sigProjMatrixToJSON	sigProjMatrixToJSON
sigScoresToJSON	sigScoresToJSON
sigsToSparseMatrix	sigsToSparseMatrix
sigsVsProjection_n	sigsVsProjection_n
sigsVsProjection_pcf	sigsVsProjection_pcf
sigsVsProjection_pcn	sigsVsProjection_pcn
sqdist	sqdist
Trajectory	Trajectory
TrajectoryProjection	TrajectoryProjection
translateCellPositions	translateCellPositions
versionCheck	versionCheck
viewResults	viewResults
viewResults,character-method	viewResults
viewResults,Vision-method	viewResults
VISION	VISION
Vision	VISION-class
Vision,data.frame-method	VISION-class
Vision,dgeMatrix-method	VISION-class
Vision,ExpressionSet-method	VISION-class
Vision,matrixORSparse-method	VISION-class
Vision,Seurat-method	VISION-class
Vision,seurat-method	VISION-class
Vision,sparseMatrix-method	VISION-class
Vision,SummarizedExperiment-method	VISION-class
