SC3: Single-Cell Consensus Clustering

A tool for unsupervised clustering and analysis of single cell RNA-Seq data.

AuthorVladimir Kiselev
Date of publicationNone
MaintainerVladimir Kiselev <vladimir.yu.kiselev@gmail.com>
LicenseGPL-3
Version1.3.14
https://github.com/hemberg-lab/SC3

View on Bioconductor

Man pages

calculate_distance: Calculate a distance matrix

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

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...

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'...

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_calc_biology: Calculate DE genes, marker genes and cell outliers.

sc3_calc_consens: Calculate consensus matrix.

sc3_calc_dists: Calculate distances between the cells.

sc3_calc_transfs: Calculate transformations of the distance matrices.

sc3_estimate_k: Estimate the optimal k for k-means clustering

sc3_export_results_xls: Write 'SC3' results to Excel file

sc3_interactive: Opens 'SC3' results in an interactive session in a web...

sc3_kmeans: 'kmeans' clustering of cells.

sc3_plot_cluster_stability: Plot stability of the clusters

sc3_plot_consensus: Plot consensus matrix as a heatmap

sc3_plot_de_genes: Plot expression of DE genes of the clusters identified by...

sc3_plot_expression: Plot expression matrix used for SC3 clustering as a heatmap

sc3_plot_markers: Plot expression of marker genes identified by 'SC3' as a...

sc3_plot_silhouette: Plot silhouette indexes of the cells

sc3_prepare: Prepare the 'SCESet' object for 'SC3' clustering.

sc3_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

treutlein: Single cell RNA-Seq data extracted from a publication by...

Functions

calculate_distance Man page
calculate_stability Man page
consensus_matrix Man page
consmx Man page
ED1 Man page
ED2 Man page
estkTW Man page
get_auroc Man page
get_biolgy Man page
get_de_genes Man page
get_marker_genes Man page
get_outl_cells Man page
get_processed_dataset Man page
markers_for_heatmap Man page
norm_laplacian Man page
organise_de_genes Man page
organise_marker_genes Man page
prepare_for_svm Man page
reindex_clusters Man page
sc3 Man page
sc3_calc_biology Man page
sc3_calc_biology, Man page
sc3_calc_biology.SCESet Man page
sc3_calc_biology,SCESet-method Man page
sc3_calc_consens Man page
sc3_calc_consens, Man page
sc3_calc_consens.SCESet Man page
sc3_calc_consens,SCESet-method Man page
sc3_calc_dists Man page
sc3_calc_dists, Man page
sc3_calc_dists.SCESet Man page
sc3_calc_dists,SCESet-method Man page
sc3_calc_transfs Man page
sc3_calc_transfs, Man page
sc3_calc_transfs.SCESet Man page
sc3_calc_transfs,SCESet-method Man page
sc3_estimate_k Man page
sc3_estimate_k.SCESet Man page
sc3_estimate_k,SCESet-method Man page
sc3_export_results_xls Man page
sc3_export_results_xls, Man page
sc3_export_results_xls.SCESet Man page
sc3_export_results_xls,SCESet-method Man page
sc3_interactive Man page
sc3_interactive, Man page
sc3_interactive.SCESet Man page
sc3_interactive,SCESet-method Man page
sc3_kmeans Man page
sc3_kmeans, Man page
sc3_kmeans.SCESet Man page
sc3_kmeans,SCESet-method Man page
sc3_plot_cluster_stability Man page
sc3_plot_cluster_stability, Man page
sc3_plot_cluster_stability.SCESet Man page
sc3_plot_cluster_stability,SCESet-method Man page
sc3_plot_consensus Man page
sc3_plot_consensus, Man page
sc3_plot_consensus.SCESet Man page
sc3_plot_consensus,SCESet-method Man page
sc3_plot_de_genes Man page
sc3_plot_de_genes, Man page
sc3_plot_de_genes.SCESet Man page
sc3_plot_de_genes,SCESet-method Man page
sc3_plot_expression Man page
sc3_plot_expression, Man page
sc3_plot_expression.SCESet Man page
sc3_plot_expression,SCESet-method Man page
sc3_plot_markers Man page
sc3_plot_markers, Man page
sc3_plot_markers.SCESet Man page
sc3_plot_markers,SCESet-method Man page
sc3_plot_silhouette Man page
sc3_plot_silhouette, Man page
sc3_plot_silhouette.SCESet Man page
sc3_plot_silhouette,SCESet-method Man page
sc3_prepare Man page
sc3_prepare.SCESet Man page
sc3_prepare,SCESet-method Man page
sc3_run_svm Man page
sc3_run_svm, Man page
sc3_run_svm.SCESet Man page
sc3_run_svm,SCESet-method Man page
sc3.SCESet Man page
sc3,SCESet-method Man page
support_vector_machines Man page
tmult Man page
transformation Man page
treutlein Man page

Files

SC3/DESCRIPTION
SC3/NAMESPACE
SC3/R
SC3/R/AllGenerics.R SC3/R/CoreFunctions.R SC3/R/CoreMethods.R SC3/R/PlotMethods.R SC3/R/RcppExports.R SC3/R/ShinyFunctions.R SC3/R/ShinyMethods.R
SC3/build
SC3/build/vignette.rds
SC3/data
SC3/data/datalist
SC3/data/treutlein.rda
SC3/inst
SC3/inst/CITATION
SC3/inst/NEWS
SC3/inst/doc
SC3/inst/doc/my-vignette.R
SC3/inst/doc/my-vignette.Rmd
SC3/inst/doc/my-vignette.html
SC3/man
SC3/man/ED1.Rd SC3/man/ED2.Rd SC3/man/calculate_distance.Rd SC3/man/calculate_stability.Rd SC3/man/consensus_matrix.Rd SC3/man/consmx.Rd SC3/man/estkTW.Rd SC3/man/get_auroc.Rd SC3/man/get_biolgy.Rd SC3/man/get_de_genes.Rd SC3/man/get_marker_genes.Rd SC3/man/get_outl_cells.Rd SC3/man/get_processed_dataset.Rd SC3/man/markers_for_heatmap.Rd SC3/man/norm_laplacian.Rd SC3/man/organise_de_genes.Rd SC3/man/organise_marker_genes.Rd SC3/man/prepare_for_svm.Rd SC3/man/reindex_clusters.Rd SC3/man/sc3.Rd SC3/man/sc3_calc_biology.Rd SC3/man/sc3_calc_consens.Rd SC3/man/sc3_calc_dists.Rd SC3/man/sc3_calc_transfs.Rd SC3/man/sc3_estimate_k.Rd SC3/man/sc3_export_results_xls.Rd SC3/man/sc3_interactive.Rd SC3/man/sc3_kmeans.Rd SC3/man/sc3_plot_cluster_stability.Rd SC3/man/sc3_plot_consensus.Rd SC3/man/sc3_plot_de_genes.Rd SC3/man/sc3_plot_expression.Rd SC3/man/sc3_plot_markers.Rd SC3/man/sc3_plot_silhouette.Rd SC3/man/sc3_prepare.Rd SC3/man/sc3_run_svm.Rd SC3/man/support_vector_machines.Rd SC3/man/tmult.Rd SC3/man/transformation.Rd SC3/man/treutlein.Rd
SC3/src
SC3/src/Makevars
SC3/src/Makevars.win
SC3/src/RcppExports.cpp
SC3/src/cppFunctions.cpp
SC3/vignettes
SC3/vignettes/my-vignette.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.