Meta-Clustering for Single-Cell Data Integration and Evaluation

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Documentation for package ‘CIDER’ version 0.99.1

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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