Minimized Single-Cell Consensus Clustering

ann | Cell type annotations for data extracted from a publication... |

calc_consensus | Calculate consensus matrix2 |

calculate_distance | Calculate a distance matrix |

calculate_stability | Calculate the stability index of the obtained clusters when... |

consensus | Consensus matrix computation |

consensus_matrix | Calculate consensus matrix |

consmx | Co-association 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 'sc3min' 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 |

sc3min | Run all steps of 'sc3min' in one go |

sc3min_calc_biology | Calculate DE genes, marker genes and cell outliers. |

sc3min_calc_consens | Calculate consensus matrix. |

sc3min_calc_dists | Calculate distances between the cells. |

sc3min_calc_transfs | Calculate transformations of the distance matrices. |

sc3min_estimate_k | Estimate the optimal number of cluster 'k' for a scRNA-Seq... |

sc3min_export_results_xls | Write 'sc3min' results to Excel file |

sc3min_interactive | Opens 'sc3min' results in an interactive session in a web... |

sc3min_kmeans | 'kmeans' clustering of cells. |

sc3min_plot_cluster_stability | Plot stability of the clusters |

sc3min_plot_consensus | Plot consensus matrix as a heatmap |

sc3min_plot_de_genes | Plot expression of DE genes of the clusters identified by... |

sc3min_plot_expression | Plot expression matrix used for sc3min clustering as a... |

sc3min_plot_markers | Plot expression of marker genes identified by 'sc3min' as a... |

sc3min_plot_silhouette | Plot silhouette indexes of the cells |

sc3min_prepare | Prepare the 'SingleCellExperiment' object for 'sc3min'... |

sc3min_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... |

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