Man pages for CamaraLab/STvEA
Spatially-resolved Transcriptomics via Epitope Anchoring

AdjScoreClustersCITEUse the Adjacency Score to evaluate colocaliztion of all...
AdjScoreClustersCITE.internalUse the Adjacency Score to evaluate colocaliztion of all...
AdjScoreClustersCODEXUse the Adjacency Score to evaluate colocaliztion of all...
AdjScoreClustersCODEX.internalUse the Adjacency Score to evaluate colocaliztion of all...
AdjScoreGenesUse the Adjacency Score to evaluate colocalization of given...
AdjScoreGenes.internalUse the Adjacency Score to evaluate colocalization of given...
AdjScoreHeatmapVisualize heatmap of Adjacency Score run on all combinations...
AdjScoreProteinsUse the Adjacency Score to evaluate colocalization of given...
AdjScoreProteins.internalUse the Adjacency Score to evaluate colocalization of given...
AnchorCorrectionRun all methods for anchor correction
CleanCITERemoves noise from CITE-seq protein data by fitting a...
CleanCITE.internalRemoves noise from CITE-seq protein data by fitting a...
CleanCODEXRemoves noise from CODEX data by fitting a Gaussian mixture...
CleanCODEX.internalRemoves noise from CODEX data by fitting a Gaussian mixture...
ClusterCODEXPerform louvain clustering on CODEX data
ClusterCODEX.internalPerform louvain clustering on CODEX data Takes matrices and...
clustering_namesAssign user input labels to clusters for future plotting
ConsensusClusterKeep only HDBSCAN results that pass a certain silhouette...
ConsensusCluster.internalKeep only HDBSCAN results that pass a certain silhouette...
ConstructNNMatConstruct nearest neighbor matrix from nn.idx
CorNNFind the knn indices in data for all cells in query using...
FilterAnchorsFilter anchors, keeping those that are also in the knn of the...
FilterCITEmRNAFilter CITE-seq mRNA data based on number of transcripts per...
FilterCITEmRNA.internalFilter CITE-seq mRNA data based on number of transcripts per...
FilterCODEXRemoves points from CODEX matrix that are not cells as...
FilterCODEX.internalRemoves points from CODEX matrix that are not cells as...
FindAnchorPairsFind Anchor pairs as MNN between two datasets
FindIntegrationMatrixCalculate anchor vectors between reference and query dataset...
FindNNFind nearest neighbors
FindNNrnaFind nearest neighbors
FindWeightsCalculates weights of the k nearest anchors for each cell in...
FitNBFits the expression values of one protein with a Negative...
GetTransferMatrixGets NN matrix for both CITE->CODEX and CODEX->CITE, stores...
GetTransferMatrix.internalGet knn in to_dataset for each cell in from_dataset based on...
GetUmapCITERuns UMAP on CITE-seq latent space (if provided) or mRNA...
GetUmapCODEXRuns UMAP on CODEX protein expression. If CleanCODEX has been...
helloHello, World!
KnnCODEXGet k nearest neighbors for CODEX protein space. If...
L2NormL2 normalize the columns (or rows) of a given matrix
MapCODEXtoCITEWraps MapCODEXtoCITE.internal using STvEA.data class
MapCODEXtoCITE.internalRun all methods for anchor correction to map the CODEX...
ParameterScanRun HDBSCAN over parameter ranges Must use Python HDBSCAN...
ParameterScan.internalRun HDBSCAN over parameter ranges Must use Python HDBSCAN...
PlotClusterCITEPlot clusters of CITE-seq cells in CITE-seq UMAP or t-SNE...
PlotClusterCODEXembPlot clusters of CODEX cells in CODEX UMAP embedding
PlotExprCITEPlot expression of a gene or protein in the CITE-seq UMAP or...
PlotExprCODEXembPlot expression of a gene or protein in the CODEX UMAP or...
PlotExprCODEXspatialPlot expression of a gene or protein in the CODEX spatial...
plot_heatmapPlot heatmap of cluster feature scores
PlotIndexCITEPlot location of a CITE-seq cell in the CITE-seq UMAP or...
PlotIndexCODEXembPlot location of a CODEX cell in the CODEX UMAP or t-SNE...
PlotIndexCODEXspatialPlot location of a CODEX cell in the CODEX spatial...
PlotSpatialNeighborsPlot the CODEX neighbors of a set of CITE-seq cells in the...
PlotSpatialRNAPlot CITE-seq gene expression on CODEX spatial coordinates
PlotUmapNeighborsPlot CITE-seq neighbors of a set of CODEX cells in the...
RunCCAThis file contains functions taken directly from the Seurat...
ScoreAnchorsScore anchors between 0 and 1 based on shared nearest...
SetDataCITESet CITE-seq data in STvEA.data object
SetDataCODEXSet CODEX data in STvEA.data object
SSECalculates the sum of squared errors in binned probabilities...
STvEA.data-classClass to hold all data matrices needed for mapping CODEX to...
STvEA-packageSTvEA: Spatially-resolved Transcriptomics via Epitope...
TransferDataSeurat2Transfer data from a Seurat object to STvEA.data object
TransformDataMatrixCorrect the query dataset by subtracting the weighted anchor...
CamaraLab/STvEA documentation built on June 5, 2019, 12:34 a.m.