Minimized Single-Cell Consensus Clustering

Vignettes

90

43

**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...**Browse all...**

If you would like to install the latest development version of SC3min please install it from the GitHub repository:

```
install.packages("devtools")
devtools::install_github("brickyyyy/SC3min")
```

brickyyyy/SC3min documentation built on May 8, 2019, 8:07 a.m.

What can we improve?

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close