SC3: Single-Cell Consensus Clustering
Version 1.4.2

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

Browse man pages Browse package API and functions Browse package files

AuthorVladimir Kiselev
Bioconductor views Classification Clustering DataRepresentation DifferentialExpression DimensionReduction GUI RNASeq SingleCell Software SupportVectorMachine Transcription Transcriptomics Visualization
Date of publicationNone
MaintainerVladimir Kiselev <vladimir.yu.kiselev@gmail.com>
LicenseGPL-3
Version1.4.2
URL https://github.com/hemberg-lab/SC3
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SC3")

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

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

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/CoreFunctions.R
R/CoreMethods.R
R/PlotMethods.R
R/RcppExports.R
R/ShinyFunctions.R
R/ShinyMethods.R
build
build/vignette.rds
data
data/datalist
data/treutlein.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/my-vignette.R
inst/doc/my-vignette.Rmd
inst/doc/my-vignette.html
man
man/ED1.Rd
man/ED2.Rd
man/calculate_distance.Rd
man/calculate_stability.Rd
man/consensus_matrix.Rd
man/consmx.Rd
man/estkTW.Rd
man/get_auroc.Rd
man/get_biolgy.Rd
man/get_de_genes.Rd
man/get_marker_genes.Rd
man/get_outl_cells.Rd
man/get_processed_dataset.Rd
man/markers_for_heatmap.Rd
man/norm_laplacian.Rd
man/organise_de_genes.Rd
man/organise_marker_genes.Rd
man/prepare_for_svm.Rd
man/reindex_clusters.Rd
man/sc3.Rd
man/sc3_calc_biology.Rd
man/sc3_calc_consens.Rd
man/sc3_calc_dists.Rd
man/sc3_calc_transfs.Rd
man/sc3_estimate_k.Rd
man/sc3_export_results_xls.Rd
man/sc3_interactive.Rd
man/sc3_kmeans.Rd
man/sc3_plot_cluster_stability.Rd
man/sc3_plot_consensus.Rd
man/sc3_plot_de_genes.Rd
man/sc3_plot_expression.Rd
man/sc3_plot_markers.Rd
man/sc3_plot_silhouette.Rd
man/sc3_prepare.Rd
man/sc3_run_svm.Rd
man/support_vector_machines.Rd
man/tmult.Rd
man/transformation.Rd
man/treutlein.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/cppFunctions.cpp
vignettes
vignettes/my-vignette.Rmd
SC3 documentation built on May 20, 2017, 9:59 p.m.