Man pages for SC3
Single-Cell Consensus Clustering
| ann | Cell type annotations for data extracted from a publication... |
| calculate_distance | Calculate a distance matrix |
| calculate_stability | Calculate the stability index of the obtained clusters when... |
| consensus_matrix | Calculate consensus matrix |
| consmx | Consensus matrix computation |
| ED1 | Compute Euclidean distance matrix by rows |
| ED2 | Compute Euclidean distance matrix by columns |
| estkTW | Estimate the optimal k for k-means clustering |
| get_auroc | Calculate the area under the ROC curve for a given gene. |
| get_biolgy | Wrapper for calculating biological properties |
| get_de_genes | Find differentially expressed genes |
| get_marker_genes | Calculate marker genes |
| get_outl_cells | Find cell outliers in each cluster. |
| get_processed_dataset | Get processed dataset used by 'SC3' clustering |
| markers_for_heatmap | Reorder and subset gene markers for plotting on a heatmap |
| norm_laplacian | Graph Laplacian calculation |
| organise_de_genes | Get differentiall expressed genes from an object of... |
| organise_marker_genes | Get marker genes from an object of 'SingleCellExperiment'... |
| prepare_for_svm | A helper function for the SVM analysis |
| reindex_clusters | Reindex cluster labels in ascending order |
| sc3 | Run all steps of 'SC3' in one go |
| sc3_calc_biology | Calculate DE genes, marker genes and cell outliers. |
| sc3_calc_consens | Calculate consensus matrix. |
| sc3_calc_dists | Calculate distances between the cells. |
| sc3_calc_transfs | Calculate transformations of the distance matrices. |
| sc3_estimate_k | Estimate the optimal number of cluster 'k' for a scRNA-Seq... |
| sc3_export_results_xls | Write 'SC3' results to Excel file |
| sc3_interactive | Opens 'SC3' results in an interactive session in a web... |
| sc3_kmeans | 'kmeans' clustering of cells. |
| sc3_plot_cluster_stability | Plot stability of the clusters |
| sc3_plot_consensus | Plot consensus matrix as a heatmap |
| sc3_plot_de_genes | Plot expression of DE genes of the clusters identified by... |
| sc3_plot_expression | Plot expression matrix used for SC3 clustering as a heatmap |
| sc3_plot_markers | Plot expression of marker genes identified by 'SC3' as a... |
| sc3_plot_silhouette | Plot silhouette indexes of the cells |
| sc3_prepare | Prepare the 'SingleCellExperiment' object for 'SC3'... |
| sc3_run_svm | Run the hybrid 'SVM' approach. |
| support_vector_machines | Run support vector machines ('SVM') prediction |
| tmult | Matrix left-multiplied by its transpose |
| transformation | Distance matrix transformation |
| yan | Single cell RNA-Seq data extracted from a publication by Yan... |
