ann |
Cell type annotations for data extracted from a publication by Yan et al. |
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' 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 'SingleCellExperiment' class |
organise_marker_genes |
Get marker genes from an object of 'SingleCellExperiment' 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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
Calculate transformations of the distance matrices. |
sc3_estimate_k |
Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix |
sc3_estimate_k-method |
Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix |
sc3_estimate_k.SingleCellExperiment |
Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix |
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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
'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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
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.SingleCellExperiment |
Plot silhouette indexes of the cells |
sc3_prepare |
Prepare the 'SingleCellExperiment' object for 'SC3' clustering. |
sc3_prepare-method |
Prepare the 'SingleCellExperiment' object for 'SC3' clustering. |
sc3_prepare.SingleCellExperiment |
Prepare the 'SingleCellExperiment' 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.SingleCellExperiment |
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 et al. |