| align_CellType | Align the cell types from the prediction with the truth. |
| cal_F2 | Calculate the gene-level F score and corresponding significance level. |
| cal_Fisher2 | Calculate the gene-level fisher score. |
| cal_metrics | Calculate 3 metrics and these methods are exported in C codes. flag = 1 - Rand index, flag = 2 - Fowlkes and Mallows's index, flag = 3 - Jaccard index |
| cal_MSE | Standard way to preprocess the count matrix. It is the QC step for the genes. |
| Consensus | Consensus Clustering |
| eval_Cluster | Calculate the a series of the evaluation statistics. |
| FEAST | FEAST main function |
| FEAST_fast | FEAST main function (fast version) |
| Norm_Y | Normalize the count expression matrix by the size factor and take the log transformation. |
| process_Y | Standard way to preprocess the count matrix. It is the QC step for the genes. |
| Purity | Calculate the purity between two vectors. |
| SC3_Clust | SC3 Clustering |
| Select_Model_short_SC3 | Using clustering results based on feature selection to perform model selection. |
| Select_Model_short_TSCAN | Using clustering results (from TSCAN) based on feature selection to perform model selection. |
| trueclass | An example single cell dataset for the cell label information (Yan) |
| TSCAN_Clust | TSCAN Clustering |
| vector2matrix | function for convert a vector to a binary matrix |
| Visual_Rslt | Using clustering results based on feature selection to perform model selection. |
| Y | An example single cell count expression matrix (Yan) |