# Improving replicability in single-cell RNA-Seq cell type discovery

## Documentation for package ‘Dune’ version 1.24.0

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

## Help Pages

.adjustedRandIndex | adjustedRandIndex
ARIImp | ARI improvement
ARIs | ARI Matrix
ARItrend | ARI improvement plot
clusMat | A clustering matrix used to demonstrate the ari-merging process.
clusterConversion | clusterConversion
ConfusionEvolution | Plot the evolution of the ConfusionPlot as merging happens
ConfusionPlot | Plot confusion matrix
Dune | Dune
Dune-method | Dune
functionTracking | Track the evolution of a function along merging
intermediateMat | Find the clustering matrix that we would get if we stopped the ARI merging early
NMIImp | NMI improvement
NMIs | NMI Matrix
NMItrend | NMI improvement plot
nuclei | Cluster labels for a subset of the allen Smart-Seq nuclei dataset
plotARIs | Plot an heatmap of the ARI matrix
plotNMIs | Plot an heatmap of the NMI matrix
plotPrePost | Plot the reduction in cluster size for an ARI merging with 'Dune'
whenToStop | When to Stop