API for YosefLab/VISION
Functional interpretation of single cell RNA-seq latent manifolds

Global functions
.colNormHelper Man page Source code
Cluster Man page Source code
NormData Man page Source code
ServerExpression Man page Source code
ServerSigProjMatrix Man page Source code
Signature Man page Source code
Trajectory Man page Source code
TrajectoryProjection Man page Source code
VISION Man page
VISION-package Man page
Vision Man page
Vision,ExpressionSet-method Man page
Vision,Seurat-method Man page
Vision,SummarizedExperiment-method Man page
Vision,data.frame-method Man page
Vision,dgeMatrix-method Man page
Vision,matrixORSparse-method Man page
Vision,seurat-method Man page
Vision,sparseMatrix-method Man page
addLatentSpace Man page Source code
addProjection Man page
addProjection,Vision-method Man page
addSignatures Man page Source code
addTSNE Man page Source code
addUMAP Man page Source code
analyze Man page
analyze,Vision-method Man page
analyzeLocalCorrelations Man page Source code
analyzeTrajectoryCorrelations Man page Source code
annotateLatentComponents Man page Source code
applyFilters Man page Source code
applyICA Man page Source code
applyISOMap Man page Source code
applyMicroClustering Man page Source code
applyPCA Man page Source code
applyPermutationWPCA Man page Source code
applyRBFPCA Man page Source code
applySimplePPT Man page Source code
applySpectralEmbedding Man page Source code
applyUMAP Man page Source code
applytSNE10 Man page Source code
applytSNE30 Man page Source code
batchSigEvalNorm Man page Source code
batchify Man page Source code
calcInterEdgeDistMat Man page Source code
calcIntraEdgeDistMat Man page Source code
calcSignatureScores Man page Source code
calculateTrajectoryDistances Man page Source code
clipBottom Man page Source code
clusterCells Man page Source code
clusterSigScores Man page Source code
clusterSignatures Man page Source code
colNormalization Man page Source code
colRankNormalization Man page Source code
colVarsSp Man page Source code
compressJSONResponse Source code
computeKNNWeights,Trajectory-method Man page
computeKNNWeights,matrix-method Man page
computeLatentSpace Man page Source code
computeProjectionGenes Man page Source code
convertGeneIds Man page Source code
coordinatesToJSON Man page Source code
createGeneSignature Man page Source code
createTrajectoryMetaData Man page Source code
evalSigGeneImportance Man page Source code
evalSigGeneImportanceSparse Man page Source code
fbConsistencyScores Man page Source code
filterGenesFano Man page Source code
filterGenesNovar Man page Source code
filterGenesThreshold Man page Source code
find_knn_parallel Man page Source code
fitTree Man page Source code
format.Vision Source code
geary Source code
geary_all Source code
geary_sig_v_proj Man page Source code
geary_sparse Source code
geary_sparse_all Source code
geary_sparse_local Source code
generatePermutationNull Man page Source code
generateProjections Man page Source code
generateProjectionsInner Man page Source code
generateTrajectoryProjections Man page Source code
getLatentSpace Man page
getLatentSpace,Vision-method Man page
getLatentTrajectory Man page
getLatentTrajectory,Vision-method Man page
getMSE Man page Source code
getMetaAutocorrelation Man page
getMetaAutocorrelation,Vision-method Man page
getMetaDifferential Man page
getMetaDifferential,Vision-method Man page
getNormalizedCopy Man page Source code
getNormalizedCopySparse Man page Source code
getParam Man page Source code
getProjections Man page
getProjections,Vision-method Man page
getSelections Man page
getSelections,Vision-method Man page
getSignatureAutocorrelation Man page
getSignatureAutocorrelation,Vision-method Man page
getSignatureDifferential Man page
getSignatureDifferential,Vision-method Man page
getSignatureScores Man page
getSignatureScores,Vision-method Man page
hasUnnormalizedData Man page Source code
ilog1p Man page Source code
innerEvalSignatureBatchNorm Man page Source code
launchServer Man page Source code
louvainCluster Man page Source code
matLog2 Man page Source code
matrix_chisq Man page Source code
matrix_wilcox Man page Source code
matrix_wilcox_cpp Man page Source code
multMat Source code
noNormalization Man page Source code
pearsonCorrToJSON Man page Source code
point_mult Source code
poolCells Man page Source code
poolMatrixCols Man page Source code
poolMatrixCols_Inner Man page Source code
poolMatrixRows Man page Source code
poolMetaData Man page Source code
print.Vision Source code
processSignatures Man page Source code
projectOnTree Man page Source code
readSignaturesInput Man page Source code
read_10x Man page Source code
read_10x_h5 Man page Source code
read_10x_h5_v2 Man page Source code
read_10x_h5_v3 Man page Source code
readjust_clusters Man page Source code
registerMethods Man page Source code
rowAndColNormalization Man page Source code
rowNormalization Man page Source code
rowVarsSp Man page Source code
saveAndViewResults Man page
saveAndViewResults,Vision-method Man page
sigConsistencyScores Man page Source code
sigGeneInner Source code
sigProjMatrixToJSON Man page Source code
sigScoresToJSON Man page Source code
signatureToJSON Man page Source code
sigsToSparseMatrix Man page Source code
sigsVsProjection_n Man page Source code
sigsVsProjection_pcf Man page Source code
sigsVsProjection_pcn Man page Source code
sqdist Man page Source code
translateCellPositions Man page Source code
versionCheck Man page Source code
viewResults Man page
viewResults,Vision-method Man page
viewResults,character-method Man page
wilcox_subset Source code
YosefLab/VISION documentation built on Nov. 22, 2019, 9:52 a.m.