Meta-Clustering for Single-Cell Data Integration and Evaluation

Documentation for package ‘CIDER’ version 0.99.0

calculateDistMatOneModel	Calculate distance matrix with in one model
cosineSimilarityR	cosine similarity in R
downsampling	Downsampling cells
estimateProb	Estimate the empirical probability of whether two set of cells from distinct batches belong to the same population
finalClustering	Final clustering step for meta-clustering
gatherInitialClusters	Gather initial cluster names
getDistMat	Calculate the Similarity Matrix
getGroupFit	Calculate IDER-based similarity between two groups
getIDEr	Compute IDER-based similarity
hdbscan.seurat	Initial clustering for evaluating integration
initialClustering	Initial clustering
measureSimilarity	Measure similarity between two vectors
mergeInitialClusters	Merge Initial Clusters
pancreas	Pancreatic scRNA-Seq data.
plotDistMat	Plot Similarity Matrix with pheatmap
plotHeatmap	Plot Heatmap for the IDER-based similarity matrix
plotNetwork	Plot Network Graph
scatterPlot	Scatterplot by a selected feature