Man pages for hemberg-lab/SC3
Single-Cell Consensus Clustering

annCell type annotations for data extracted from a publication...
calculate_distanceCalculate a distance matrix
calculate_stabilityCalculate the stability index of the obtained clusters when...
consensus_matrixCalculate consensus matrix
consmxConsensus matrix computation
ED1Compute Euclidean distance matrix by rows
ED2Compute Euclidean distance matrix by columns
estkTWEstimate the optimal k for k-means clustering
get_aurocCalculate the area under the ROC curve for a given gene.
get_biolgyWrapper for calculating biological properties
get_de_genesFind differentially expressed genes
get_marker_genesCalculate marker genes
get_outl_cellsFind cell outliers in each cluster.
get_processed_datasetGet processed dataset used by 'SC3' clustering
markers_for_heatmapReorder and subset gene markers for plotting on a heatmap
norm_laplacianGraph Laplacian calculation
organise_de_genesGet differentiall expressed genes from an object of...
organise_marker_genesGet marker genes from an object of 'SingleCellExperiment'...
prepare_for_svmA helper function for the SVM analysis
reindex_clustersReindex cluster labels in ascending order
sc3Run all steps of 'SC3' in one go
sc3_calc_biologyCalculate DE genes, marker genes and cell outliers.
sc3_calc_consensCalculate consensus matrix.
sc3_calc_distsCalculate distances between the cells.
sc3_calc_transfsCalculate transformations of the distance matrices.
sc3_estimate_kEstimate the optimal number of cluster 'k' for a scRNA-Seq...
sc3_export_results_xlsWrite 'SC3' results to Excel file
sc3_interactiveOpens 'SC3' results in an interactive session in a web...
sc3_kmeans'kmeans' clustering of cells.
sc3_plot_cluster_stabilityPlot stability of the clusters
sc3_plot_consensusPlot consensus matrix as a heatmap
sc3_plot_de_genesPlot expression of DE genes of the clusters identified by...
sc3_plot_expressionPlot expression matrix used for SC3 clustering as a heatmap
sc3_plot_markersPlot expression of marker genes identified by 'SC3' as a...
sc3_plot_silhouettePlot silhouette indexes of the cells
sc3_preparePrepare the 'SingleCellExperiment' object for 'SC3'...
sc3_run_svmRun the hybrid 'SVM' approach.
support_vector_machinesRun support vector machines ('SVM') prediction
tmultMatrix left-multiplied by its transpose
transformationDistance matrix transformation
yanSingle cell RNA-Seq data extracted from a publication by Yan...
hemberg-lab/SC3 documentation built on May 11, 2018, 4:32 p.m.