Man pages for CamaraLab/STvEA
Spatially-resolved Transcriptomics via Epitope Anchoring
| AdjScoreClustersCITE | Use the Adjacency Score to evaluate colocaliztion of all... |
| AdjScoreClustersCITE.internal | Use the Adjacency Score to evaluate colocaliztion of all... |
| AdjScoreClustersCODEX | Use the Adjacency Score to evaluate colocaliztion of all... |
| AdjScoreClustersCODEX.internal | Use the Adjacency Score to evaluate colocaliztion of all... |
| AdjScoreGenes | Use the Adjacency Score to evaluate colocalization of given... |
| AdjScoreGenes.internal | Use the Adjacency Score to evaluate colocalization of given... |
| AdjScoreHeatmap | Visualize heatmap of Adjacency Score run on all combinations... |
| AdjScoreProteins | Use the Adjacency Score to evaluate colocalization of given... |
| AdjScoreProteins.internal | Use the Adjacency Score to evaluate colocalization of given... |
| AnchorCorrection | Run all methods for anchor correction |
| CleanCITE | Removes noise from CITE-seq protein data by fitting a two... |
| CleanCITE.gaussian.internal | Removes noise from CITE-seq protein data by fitting a... |
| CleanCITE.nb.internal | Removes noise from CITE-seq protein data by fitting a... |
| CleanCODEX | Removes noise from CODEX data by fitting a Gaussian mixture... |
| CleanCODEX.gaussian.internal | Removes noise from CODEX data by fitting a Gaussian mixture... |
| CleanCODEX.nb.internal | Removes noise from CODEX protein data by fitting a... |
| ClusterCODEX | Perform louvain clustering on CODEX data |
| ClusterCODEX.internal | Perform louvain clustering on CODEX data Takes matrices and... |
| clustering_names | Assign user input labels to clusters for future plotting |
| ConsensusCluster | Keep only HDBSCAN results that pass a certain silhouette... |
| ConsensusCluster.internal | Keep only HDBSCAN results that pass a certain silhouette... |
| ConstructNNMat | Construct nearest neighbor matrix from nn.idx |
| CorNN | Find the knn indices in data for all cells in query using... |
| FilterAnchors | Filter anchors, keeping those that are also in the knn of the... |
| FilterCITEmRNA | Filter CITE-seq mRNA data based on number of transcripts per... |
| FilterCITEmRNA.internal | Filter CITE-seq mRNA data based on number of transcripts per... |
| FilterCODEX | Removes points from CODEX matrix that are not cells as... |
| FilterCODEX.internal | Removes points from CODEX matrix that are not cells as... |
| FindAnchorPairs | Find Anchor pairs as MNN between two datasets |
| FindIntegrationMatrix | Calculate anchor vectors between reference and query dataset... |
| FindNN | Find nearest neighbors |
| FindNNrna | Find nearest neighbors |
| FindWeights | Calculates weights of the k nearest anchors for each cell in... |
| FitGaussian | Fits the log-normalized expression values of one protein with... |
| FitNB | Fits the expression values of one protein with a Negative... |
| GetTransferMatrix | Gets NN matrix for CITE->CODEX, stores in STvEA.data |
| GetTransferMatrix.internal | Get knn in to_dataset for each cell in from_dataset based on... |
| GetUmapCITE | Runs UMAP on CITE-seq latent space (if provided) or mRNA... |
| GetUmapCODEX | Runs UMAP on CODEX protein expression. If CleanCODEX has been... |
| hello | Hello, World! |
| KnnCODEX | Get k nearest neighbors for CODEX protein space. If... |
| L2Norm | L2 normalize the columns (or rows) of a given matrix |
| MapCODEXtoCITE | Wraps MapCODEXtoCITE.internal using STvEA.data class |
| MapCODEXtoCITE.internal | Run all methods for anchor correction to map the CODEX... |
| NormCells | Normalize protein matrix by dividing out total counts per... |
| ParameterScan | Run HDBSCAN over parameter ranges Must use Python HDBSCAN... |
| ParameterScan.internal | Run HDBSCAN over parameter ranges Must use Python HDBSCAN... |
| PlotClusterCITE | Plot clusters of CITE-seq cells in CITE-seq UMAP or t-SNE... |
| PlotClusterCODEXemb | Plot clusters of CODEX cells in CODEX UMAP embedding |
| PlotExprCITE | Plot expression of a gene or protein in the CITE-seq UMAP or... |
| PlotExprCODEXemb | Plot expression of a gene or protein in the CODEX UMAP or... |
| PlotExprCODEXspatial | Plot expression of a gene or protein in the CODEX spatial... |
| PlotIndexCITE | Plot location of a CITE-seq cell in the CITE-seq UMAP or... |
| PlotIndexCODEXemb | Plot location of a CODEX cell in the CODEX UMAP or t-SNE... |
| PlotIndexCODEXspatial | Plot location of a CODEX cell in the CODEX spatial... |
| ReadDataFCS | Read in FCS file |
| ReadNamesFCS | Reads channel names from FCS two different ways |
| RunCCA | This file contains functions taken directly from the Seurat... |
| ScoreAnchors | Score anchors between 0 and 1 based on shared nearest... |
| SetDataCITE | Set CITE-seq data in STvEA.data object |
| SetDataCODEX | Set CODEX data in STvEA.data object |
| SSE | Calculates the sum of squared errors in binned probabilities... |
| STvEA.data-class | Class to hold all data matrices needed for mapping CODEX to... |
| STvEA-package | STvEA: Spatially-resolved Transcriptomics via Epitope... |
| TransferDataSeurat2 | Transfer data from a Seurat object to STvEA.data object |
| TransformDataMatrix | Correct the query dataset by subtracting the weighted anchor... |
