Package: SC3 1.35.0

Vladimir Kiselev

SC3: Single-Cell Consensus Clustering

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

Authors:Vladimir Kiselev

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SC3.pdf |SC3.html✨
SC3/json (API)
NEWS

# Install 'SC3' in R:

install.packages('SC3', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hemberg-lab/sc3/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

ann - Cell type annotations for data extracted from a publication by Yan et al.
yan - Single cell RNA-Seq data extracted from a publication by Yan et al.

On BioConductor:SC3-1.35.0(bioc 3.21)SC3-1.34.0(bioc 3.20)

immunooncology singlecell software classification clustering dimensionreduction supportvectormachine rnaseq visualization transcriptomics datarepresentation gui differentialexpression transcription bioconductor-package human-cell-atlas single-cell-rna-seq openblas cpp

10.08 score 119 stars 1 packages 370 scripts 608 downloads 71 mentions 24 exports 99 dependencies

Last updated 2 months agofrom:9b5ac20f8a. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 25 2024
R-4.5-win-x86_64	NOTE	Nov 25 2024
R-4.5-linux-x86_64	NOTE	Nov 25 2024
R-4.4-win-x86_64	NOTE	Nov 25 2024
R-4.4-mac-x86_64	NOTE	Nov 25 2024
R-4.4-mac-aarch64	NOTE	Nov 25 2024
R-4.3-win-x86_64	NOTE	Nov 25 2024
R-4.3-mac-x86_64	NOTE	Nov 25 2024
R-4.3-mac-aarch64	NOTE	Nov 25 2024

Exports:consensus_matrix get_de_genes get_marker_genes get_outl_cells get_processed_dataset norm_laplacian reindex_clusters sc3 sc3_calc_biology sc3_calc_consens sc3_calc_dists sc3_calc_transfs sc3_estimate_k sc3_export_results_xls sc3_interactive sc3_kmeans sc3_plot_cluster_stability sc3_plot_consensus sc3_plot_de_genes sc3_plot_expression sc3_plot_markers sc3_plot_silhouette sc3_prepare sc3_run_svm

Dependencies:abind askpass base64enc Biobase BiocGenerics bitops bslib cachem caTools class cli cluster codetools colorspace commonmark crayon curl DelayedArray DEoptimR digest doParallel doRNG e1071 fansi farver fastmap fontawesome foreach fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gplots gtable gtools htmltools httpuv httr IRanges isoband iterators jquerylib jsonlite KernSmooth labeling later lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell mvtnorm nlme openssl pcaPP pheatmap pillar pkgconfig promises proxy R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang rngtools robustbase ROCR rrcov S4Arrays S4Vectors sass scales shiny SingleCellExperiment sourcetools SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr WriteXLS xtable XVector zlibbioc

SC3 package manual

Vladimir Kiselev

Rendered fromSC3.Rmdusingknitr::rmarkdownon Nov 25 2024.

Last update: 2023-05-15
Started: 2017-10-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cell type annotations for data extracted from a publication by Yan et al.	ann
Calculate a distance matrix	calculate_distance
Calculate the stability index of the obtained clusters when changing 'k'	calculate_stability
Calculate consensus matrix	consensus_matrix
Consensus matrix computation	consmx
Compute Euclidean distance matrix by rows	ED1
Compute Euclidean distance matrix by columns	ED2
Estimate the optimal k for k-means clustering	estkTW
Calculate the area under the ROC curve for a given gene.	get_auroc
Wrapper for calculating biological properties	get_biolgy
Find differentially expressed genes	get_de_genes
Calculate marker genes	get_marker_genes
Find cell outliers in each cluster.	get_outl_cells
Get processed dataset used by 'SC3' clustering	get_processed_dataset
Reorder and subset gene markers for plotting on a heatmap	markers_for_heatmap
Graph Laplacian calculation	norm_laplacian
Get differentiall expressed genes from an object of 'SingleCellExperiment' class	organise_de_genes
Get marker genes from an object of 'SingleCellExperiment' class	organise_marker_genes
A helper function for the SVM analysis	prepare_for_svm
Reindex cluster labels in ascending order	reindex_clusters
Run all steps of 'SC3' in one go	sc3 sc3,SingleCellExperiment-method sc3.SingleCellExperiment
Calculate DE genes, marker genes and cell outliers.	sc3_calc_biology sc3_calc_biology, sc3_calc_biology,SingleCellExperiment-method sc3_calc_biology.SingleCellExperiment
Calculate consensus matrix.	sc3_calc_consens sc3_calc_consens, sc3_calc_consens,SingleCellExperiment-method sc3_calc_consens.SingleCellExperiment
Calculate distances between the cells.	sc3_calc_dists sc3_calc_dists, sc3_calc_dists,SingleCellExperiment-method sc3_calc_dists.SingleCellExperiment
Calculate transformations of the distance matrices.	sc3_calc_transfs sc3_calc_transfs, sc3_calc_transfs,SingleCellExperiment-method sc3_calc_transfs.SingleCellExperiment
Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix	sc3_estimate_k sc3_estimate_k,SingleCellExperiment-method sc3_estimate_k.SingleCellExperiment
Write 'SC3' results to Excel file	sc3_export_results_xls sc3_export_results_xls,SingleCellExperiment-method sc3_export_results_xls.SingleCellExperiment
Opens 'SC3' results in an interactive session in a web browser.	sc3_interactive sc3_interactive, sc3_interactive,SingleCellExperiment-method sc3_interactive.SingleCellExperiment
'kmeans' clustering of cells.	sc3_kmeans sc3_kmeans, sc3_kmeans,SingleCellExperiment-method sc3_kmeans.SingleCellExperiment
Plot stability of the clusters	sc3_plot_cluster_stability sc3_plot_cluster_stability, sc3_plot_cluster_stability,SingleCellExperiment-method sc3_plot_cluster_stability.SingleCellExperiment
Plot consensus matrix as a heatmap	sc3_plot_consensus sc3_plot_consensus, sc3_plot_consensus,SingleCellExperiment-method sc3_plot_consensus.SingleCellExperiment
Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap	sc3_plot_de_genes sc3_plot_de_genes, sc3_plot_de_genes,SingleCellExperiment-method sc3_plot_de_genes.SingleCellExperiment
Plot expression matrix used for SC3 clustering as a heatmap	sc3_plot_expression sc3_plot_expression, sc3_plot_expression,SingleCellExperiment-method sc3_plot_expression.SingleCellExperiment
Plot expression of marker genes identified by 'SC3' as a heatmap.	sc3_plot_markers sc3_plot_markers, sc3_plot_markers,SingleCellExperiment-method sc3_plot_markers.SingleCellExperiment
Plot silhouette indexes of the cells	sc3_plot_silhouette sc3_plot_silhouette, sc3_plot_silhouette,SingleCellExperiment-method sc3_plot_silhouette.SingleCellExperiment
Prepare the 'SingleCellExperiment' object for 'SC3' clustering.	sc3_prepare sc3_prepare,SingleCellExperiment-method sc3_prepare.SingleCellExperiment
Run the hybrid 'SVM' approach.	sc3_run_svm sc3_run_svm, sc3_run_svm,SingleCellExperiment-method sc3_run_svm.SingleCellExperiment
Run support vector machines ('SVM') prediction	support_vector_machines
Matrix left-multiplied by its transpose	tmult
Distance matrix transformation	transformation
Single cell RNA-Seq data extracted from a publication by Yan et al.	yan