# Single-Cell Consensus Clustering

## Documentation for package ‘SC3’ version 1.4.2

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

## Help Pages

calculate_distance | Calculate a distance matrix
calculate_stability | Calculate the stability index of the obtained clusters when changing k
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 from the default scater slots
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 'SCESet' class
organise_marker_genes | Get marker genes from an object of 'SCESet' class
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-method | Run all steps of 'SC3' in one go
sc3.SCESet | Run all steps of 'SC3' in one go
sc3_calc_biology | Calculate DE genes, marker genes and cell outliers.
sc3_calc_biology, | Calculate DE genes, marker genes and cell outliers.
sc3_calc_biology-method | Calculate DE genes, marker genes and cell outliers.
sc3_calc_biology.SCESet | Calculate DE genes, marker genes and cell outliers.
sc3_calc_consens | Calculate consensus matrix.
sc3_calc_consens, | Calculate consensus matrix.
sc3_calc_consens-method | Calculate consensus matrix.
sc3_calc_consens.SCESet | Calculate consensus matrix.
sc3_calc_dists | Calculate distances between the cells.
sc3_calc_dists, | Calculate distances between the cells.
sc3_calc_dists-method | Calculate distances between the cells.
sc3_calc_dists.SCESet | Calculate distances between the cells.
sc3_calc_transfs | Calculate transformations of the distance matrices.
sc3_calc_transfs, | Calculate transformations of the distance matrices.
sc3_calc_transfs-method | Calculate transformations of the distance matrices.
sc3_calc_transfs.SCESet | Calculate transformations of the distance matrices.
sc3_estimate_k | Estimate the optimal k for k-means clustering
sc3_estimate_k-method | Estimate the optimal k for k-means clustering
sc3_estimate_k.SCESet | Estimate the optimal k for k-means clustering
sc3_export_results_xls | Write 'SC3' results to Excel file
sc3_export_results_xls, | Write 'SC3' results to Excel file
sc3_export_results_xls-method | Write 'SC3' results to Excel file
sc3_export_results_xls.SCESet | Write 'SC3' results to Excel file
sc3_interactive | Opens 'SC3' results in an interactive session in a web browser.
sc3_interactive, | Opens 'SC3' results in an interactive session in a web browser.
sc3_interactive-method | Opens 'SC3' results in an interactive session in a web browser.
sc3_interactive.SCESet | Opens 'SC3' results in an interactive session in a web browser.
sc3_kmeans | 'kmeans' clustering of cells.
sc3_kmeans, | 'kmeans' clustering of cells.
sc3_kmeans-method | 'kmeans' clustering of cells.
sc3_kmeans.SCESet | 'kmeans' clustering of cells.
sc3_plot_cluster_stability | Plot stability of the clusters
sc3_plot_cluster_stability, | Plot stability of the clusters
sc3_plot_cluster_stability-method | Plot stability of the clusters
sc3_plot_cluster_stability.SCESet | Plot stability of the clusters
sc3_plot_consensus | Plot consensus matrix as a heatmap
sc3_plot_consensus, | Plot consensus matrix as a heatmap
sc3_plot_consensus-method | Plot consensus matrix as a heatmap
sc3_plot_consensus.SCESet | Plot consensus matrix as a heatmap
sc3_plot_de_genes | Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_de_genes, | Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_de_genes-method | Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_de_genes.SCESet | Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_expression | Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_expression, | Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_expression-method | Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_expression.SCESet | Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_markers | Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_markers, | Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_markers-method | Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_markers.SCESet | Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_silhouette | Plot silhouette indexes of the cells
sc3_plot_silhouette, | Plot silhouette indexes of the cells
sc3_plot_silhouette-method | Plot silhouette indexes of the cells
sc3_plot_silhouette.SCESet | Plot silhouette indexes of the cells
sc3_prepare | Prepare the 'SCESet' object for 'SC3' clustering.
sc3_prepare-method | Prepare the 'SCESet' object for 'SC3' clustering.
sc3_prepare.SCESet | Prepare the 'SCESet' object for 'SC3' clustering.
sc3_run_svm | Run the hybrid 'SVM' approach.
sc3_run_svm, | Run the hybrid 'SVM' approach.
sc3_run_svm-method | Run the hybrid 'SVM' approach.
sc3_run_svm.SCESet | 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
treutlein | Single cell RNA-Seq data extracted from a publication by Treutlein et al.