SC3: Single-Cell Consensus Clustering

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

Author
Vladimir Kiselev
Date of publication
None
Maintainer
Vladimir Kiselev <vladimir.yu.kiselev@gmail.com>
License
GPL-3
Version
1.3.6
URLs

View on Bioconductor

Man pages

calculate_distance
Calculate a distance matrix
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
gene_filter
Gene filter
get_de_genes
Find differentially expressed genes
get_marker_genes
Find marker genes
get_outl_cells
Find cell outliers
get_processed_dataset
Get processed dataset used by SC3 from the default scater...
iwanthue
Generate a colour palette by k-means clustering of LAB colour...
norm_laplacian
Graph Laplacian calculation
prepare_for_svm
A helper function for the SVM analysis
sc3_calc_biology.SCESet
Calculate DE genes, marker genes and cell outliers.
sc3_calc_consens.SCESet
Calculate consensus matrix.
sc3_calc_dists.SCESet
Calculate distances between the cells.
sc3_calc_transfs.SCESet
Calculate transformations of the distance matrices.
sc3_estimate_k.SCESet
Estimate the optimal k for k-means clustering
sc3_export_results_xls.SCESet
Write SC3 results to Excel file
sc3_interactive.SCESet
Open SC3 results in an interactive session in a web browser
sc3_kmeans.SCESet
kmeans clustering of the transformed distance matrices.
sc3_plot_cell_outliers.SCESet
Plot cell outliers
sc3_plot_cluster_stability.SCESet
Plot stability of the clusters
sc3_plot_consensus.SCESet
Plot consensus matrix as a heatmap
sc3_plot_de_genes.SCESet
Plot expression of DE genes of the clusters identified by SC3...
sc3_plot_expression.SCESet
Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_markers.SCESet
Plot expression of marker genes of the clusters identified by...
sc3_plot_silhouette.SCESet
Plot silhouette indexes of the cells
sc3_plot_tsne.SCESet
Plot tSNE map of the cells and highlight SC3 clusters with...
sc3_prepare.SCESet
Prepare the SCESet object for SC3 clustering
sc3_run_svm.SCESet
Run SVM on training cells
sc3.SCESet
Run all steps of SC3 in one go
sc3_set_ks.SCESet
Sets a range of the number of clusters k used for SC3...
sc3_summarise_results.SCESet
Summarise SC3 results
StabilityIndex
Calculate the stability index of the obtained clusters when...
support_vector_machines
Run support vector machines (SVM) prediction
swatch
Plot colour swatches for a vector of colours
tmult
Matrix left-multiplied by its transpose
transformation
Distance matrix transformation
treutlein
Single cell RNA-Seq data extracted from a publication by...

Files in this package

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/R/Utils.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/StabilityIndex.Rd
SC3/man/calculate_distance.Rd
SC3/man/consensus_matrix.Rd
SC3/man/consmx.Rd
SC3/man/estkTW.Rd
SC3/man/gene_filter.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/iwanthue.Rd
SC3/man/norm_laplacian.Rd
SC3/man/prepare_for_svm.Rd
SC3/man/sc3.SCESet.Rd
SC3/man/sc3_calc_biology.SCESet.Rd
SC3/man/sc3_calc_consens.SCESet.Rd
SC3/man/sc3_calc_dists.SCESet.Rd
SC3/man/sc3_calc_transfs.SCESet.Rd
SC3/man/sc3_estimate_k.SCESet.Rd
SC3/man/sc3_export_results_xls.SCESet.Rd
SC3/man/sc3_interactive.SCESet.Rd
SC3/man/sc3_kmeans.SCESet.Rd
SC3/man/sc3_plot_cell_outliers.SCESet.Rd
SC3/man/sc3_plot_cluster_stability.SCESet.Rd
SC3/man/sc3_plot_consensus.SCESet.Rd
SC3/man/sc3_plot_de_genes.SCESet.Rd
SC3/man/sc3_plot_expression.SCESet.Rd
SC3/man/sc3_plot_markers.SCESet.Rd
SC3/man/sc3_plot_silhouette.SCESet.Rd
SC3/man/sc3_plot_tsne.SCESet.Rd
SC3/man/sc3_prepare.SCESet.Rd
SC3/man/sc3_run_svm.SCESet.Rd
SC3/man/sc3_set_ks.SCESet.Rd
SC3/man/sc3_summarise_results.SCESet.Rd
SC3/man/support_vector_machines.Rd
SC3/man/swatch.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