| SCIntRuler-package | SCIntRuler: Integration of Single-Cell RNA-seq Datasets |
| CalcuSCIR | Calculate SCIntRuler |
| crossdist | Cross-Distance Matrix Calculation |
| FindCell | Find cells indicating shared biological features across conditions |
| FindNNDist | Find the nearest neighbors |
| FindNNDistC | Find the nearest neighbors |
| GetCluster | Get broad and fine clusters |
| NormData | Normalized RNA data matrix |
| PermTest | Permutation Test |
| PlotSCIR | Plot SCIntRuler |
| SCEtoSeurat | Input and Split SingleCellExperiment Data |
| SCIntRuler | SCIntRuler: Integration of Single-Cell RNA-seq Datasets |
| sim_data_sce | My Example Dataset |
| sim_result | My Example Dataset |
| SummCluster | Get maximum number of broad clusters |