# Meta-Clustering for Single-Cell Data Integration and Evaluation

## Documentation for package ‘CIDER’ version 0.99.0

- DESCRIPTION file.

## Help Pages

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