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... |
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