# Meta-Clustering for scRNA-Seq Integration and Evaluation

## Documentation for package ‘CIDER’ version 0.99.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calculateDistMatOneModel | Calculate Distance Matrix Using a Single Model
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
mergeInitialClusters | Merge Initial Clusters
pancreas_meta | Pancreas Metadata
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