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

addLatentSpaceAdd a latent space computed using an external method
addProjection-Vision-methodAdd a set of projection coordinates to use for visualization
addSignaturesAdd signatures to VISION object
addTSNEAdds a tSNE projection
addUMAPAdds a UMAP projection
analyzeLocalCorrelationsCompute local correlations for all signatures
analyzeTrajectoryCorrelationsCompute trajectory correlations for all signatures
analyze-Vision-methodMain entry point for running VISION Analysis
annotateLatentComponentsCompute pearson correlation between signature scores and...
applyFiltersApplies filters to the inputted expression data (may remove...
applyICAPerforms ICA on data
applyISOMapPerforms ISOMap on data
applyMicroClusteringPool cells into microclusters
applyPCAPerforms PCA on data
applyPermutationWPCAApplies pemutation method to return the most significant...
applyRBFPCAPerforms PCA on data that has been transformed with the...
applySimplePPTApplies the Simple PPT algorithm onto the expression data.
applySpectralEmbeddingPerforms Spectral Embedding on data
applytSNE10Performs tSNE with perplexity 10 on data
applytSNE30Performs tSNE with perplexity 30 on data
applyUMAPPerforms UMAP on data
batchifyUtility methods Helper utility to group list items into...
batchSigEvalNormEvaluate signature scores efficiently in batches
calcInterEdgeDistMatCalculate all distances between points on two different edges
calcIntraEdgeDistMatCalculate distances between all points on a given edge,...
calcSignatureScorescalculate signature scores
calculateTrajectoryDistancesCalculate distance matrix between all pairs of ponts based on...
clipBottomSets all values below a certain level in the data equal to 0
ClusterWrapper class for a particular cluster. Maps a cluster type...
clusterCellsCreates clustering of the cells
clusterSignaturesClusters signatures according to the rank sum
clusterSigScoresCompute Ranksums Test, for all factor meta data. One level...
colNormalizationPerforms z-normalization on all columns
colRankNormalizationCreaes a new version of the data that has ranks (column-wise)...
colVarsSpCompute col-wise variance on matrix without densifying
computeKNNWeights-matrix-methodcompute for each vector the weights to apply to it's K...
computeKNNWeights-Trajectory-methodCompute KNN weights based on geodesic distances for...
computeLatentSpaceComputes the latent space of the expression matrix using PCA
computeProjectionGenesfilter data accourding to the provided filters
convertGeneIdsChange Gene Identifiers
coordinatesToJSONConverts a projection into a JSON object mapping each sample...
createGeneSignatureCreate a user-defined gene signature
createTrajectoryMetaDataGenerate meta-data associated with this trajectory
dot-colNormHelperCalculates the column znormalization after row znormalization
evalSigGeneImportanceCalculate gene-signature importance
evalSigGeneImportanceSparseCalculate Gene-Signature Importance
fbConsistencyScoresEvaluates the significance of each protein
filterGenesFanoApplies the Fano filter to the input data (may remove rows)
filterGenesNovarEliminate genes whose sample variance is equal to 0 (may...
filterGenesThresholdFilter genes whose values sum to less than some threshold...
find_knn_parallelParallel KNN
fitTreeFit tree using input parameters
geary_sig_v_projEvaluates values vs coordinates using the Geary C
generatePermutationNullGenerate random signatures for a null distribution by...
generateProjectionsgenerate projections
generateProjectionsInnerProjects data into 2 dimensions using a variety of linear and...
generateTrajectoryProjectionsGenerate 2d representations of a trajectory model
getLatentSpaceGet Latent Space
getLatentTrajectoryGet Latent Trajectory
getMetaAutocorrelationGet MetaData Autocorrelation Scores
getMetaDifferentialGet Results of One-vs-All Differential Tests with Metadata...
getMSECalculates the MSE between C and X
getNormalizedCopyCalculates the specified normalized data matrix
getNormalizedCopySparseCalculates the specified normalized data matrix
getParamGets parameters with defaults
getProjectionsGet 2D views of the expression data
getSelectionsGet saved selections
getSignatureAutocorrelationGet Signature Autocorrelation Scores
getSignatureDifferentialGet Results of One-vs-All Differential Signature Tests
getSignatureScoresGet Signature Scores
hasUnnormalizedDataTests for Unnormalized Data
ilog1pinverse log-scale transform a dense OR sparse matrix
innerEvalSignatureBatchNormUsed in inner loop of batchSigEvalNorm
launchServerLanch the server
louvainClusterApplies the Louvain algorithm to generate micro-clustered...
matLog2log2-scale transform a dense OR sparse matrix
matrix_chisqPerform 1vAll factor analysis given a factor matrix and group...
matrix_wilcoxVectorized wilcox rank-sums test
matrix_wilcox_cppC++ wilcox rank-sums test
noNormalizationDoes nothing, just returns the original data
NormDataInitialize a new NormData object
pearsonCorrToJSONconvert perason correlation coeffcients between PCs and...
poolCellscreate micro-clusters that reduce noise and complexity while...
poolMatrixColsPools columns of a numeric matrix
poolMatrixCols_Innercreate "super-cells" by pooling together single cells
poolMatrixRowsPools rows of a numeric matrix
poolMetaDataAggregate meta-data for cells in pools
processSignaturesProcesses signatures on input
projectOnTreeProject the given dataoints onto the tree defined by the...
read_10xRead 10x Output
read_10x_h5Read 10x HDF5 Output
read_10x_h5_v2Read 10x HDF5 Output - CellRanger 2.0
read_10x_h5_v3Read 10x HDF5 Output - CellRanger 3.0
readjust_clustersRepartitions existing clusters to achieve desired...
readSignaturesInputReads in a list of signature input files.
registerMethodsRegisters the projection methods to be used
rowAndColNormalizationPerforms z-normalization on all columns and rows
rowNormalizationPerforms z-normalization on all rows
rowVarsSpCompute row-wise variance on matrix without densifying
saveAndViewResults-Vision-methodSave the VISION object as an .RDS file and view the results...
ServerExpressionWrapper class for gene expression object for JSON.
ServerSigProjMatrixWrapper class for Signature Projection Matrix
sigConsistencyScoresEvaluates the significance of each signature in each cluster
SignatureInitialize a new Signature object.
signatureToJSONConverts Signature object to JSON
sigProjMatrixToJSONConverts a sigProjMatrix from an R Object to a JSON object
sigScoresToJSONConverts row of sigantures score matrix to JSON
sigsToSparseMatrixUtility method to load signatures into a sparse matrix
sigsVsProjection_nEvaluates the significance of each numeric signature vs. a...
sigsVsProjection_pcfEvaluates the significance of each meta data factor signature...
sigsVsProjection_pcnEvaluates the significance of each meta data numeric...
sqdistAlternative computation of distance matrix, based on matrix...
TrajectoryInitialize a new Trajectory object.
TrajectoryProjectionInitialize a new TrajectoryProjection object.
translateCellPositionsTranslate cell positions
versionCheckChecks the version of the Vision object and displays error if...
viewResultsView results of analysis
VISION-classInitializes a new VISION object.
YosefLab/VISION documentation built on Dec. 7, 2019, 8:16 p.m.