Introduction | SingleCellExperiment, QC and scater | Quick Start | SC3 Input | Run SC3 | colData | rowData | Number of Сells | Plot Functions | Consensus Matrix | Silhouette Plot | Expression Matrix | Cluster Stability | DE genes | Marker Genes | SC3 in Detail | sc3_prepare | (optional) sc3_estimate_k | sc3_calc_dists | sc3_calc_transfs | sc3_kmeans | sc3_calc_consens | (optional) sc3_calc_biology | Cell Outliers | DE and marker genes | Hybrid SVM Approach
Package: SC3 1.41.0
Vladimir Kiselev
SC3: Single-Cell Consensus Clustering
A tool for unsupervised clustering and analysis of single cell RNA-Seq data.
Authors:
SC3_1.41.0.tar.gz
SC3_1.41.0.zip(r-4.7)SC3_1.41.0.zip(r-4.6)SC3_1.41.0.zip(r-4.5)
SC3_1.41.0.tgz(r-4.6-x86_64)SC3_1.41.0.tgz(r-4.6-arm64)SC3_1.41.0.tgz(r-4.5-x86_64)SC3_1.41.0.tgz(r-4.5-arm64)
SC3_1.41.0.tar.gz(r-4.7-arm64)SC3_1.41.0.tar.gz(r-4.7-x86_64)SC3_1.41.0.tar.gz(r-4.6-arm64)SC3_1.41.0.tar.gz(r-4.6-x86_64)
SC3_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SC3/json (API)
| # 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
Datasets:
On BioConductor:SC3-1.41.0(bioc 3.24)SC3-1.40.0(bioc 3.23)
immunooncologysinglecellsoftwareclassificationclusteringdimensionreductionsupportvectormachinernaseqvisualizationtranscriptomicsdatarepresentationguidifferentialexpressiontranscriptionbioconductor-packagehuman-cell-atlassingle-cell-rna-seqopenblascpp
Last updated from:05b84c47da. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 211 | ||
| linux-devel-arm64 | NOTE | 282 | ||
| linux-devel-x86_64 | NOTE | 354 | ||
| source / vignettes | OK | 752 | ||
| linux-release-arm64 | NOTE | 287 | ||
| linux-release-x86_64 | NOTE | 368 | ||
| macos-release-arm64 | NOTE | 184 | ||
| macos-release-x86_64 | NOTE | 508 | ||
| macos-oldrel-arm64 | NOTE | 240 | ||
| macos-oldrel-x86_64 | NOTE | 460 | ||
| windows-devel | NOTE | 327 | ||
| windows-release | NOTE | 277 | ||
| windows-oldrel | NOTE | 257 | ||
| wasm-release | OK | 203 |
Exports:consensus_matrixget_de_genesget_marker_genesget_outl_cellsget_processed_datasetnorm_laplacianreindex_clusterssc3sc3_calc_biologysc3_calc_consenssc3_calc_distssc3_calc_transfssc3_estimate_ksc3_export_results_xlssc3_interactivesc3_kmeanssc3_plot_cluster_stabilitysc3_plot_consensussc3_plot_de_genessc3_plot_expressionsc3_plot_markerssc3_plot_silhouettesc3_preparesc3_run_svm
Dependencies:abindbase64encBiobaseBiocGenericsbitopsbslibcachemcaToolsclasscliclustercodetoolscommonmarkcpp11DelayedArrayDEoptimRdigestdoParalleldoRNGe1071farverfastmapfontawesomeforeachfsgenericsGenomicRangesggplot2gluegplotsgtablegtoolshtmltoolshttpuvIRangesisobanditeratorsjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormotelpcaPPpheatmappromisesproxyR6rappdirsRColorBrewerRcppRcppArmadillorlangrngtoolsrobustbaseROCRrrcovS4ArraysS4VectorsS7sassscalesSeqinfoshinySingleCellExperimentsourcetoolsSparseArraySummarizedExperimentvctrsviridisLitewithrWriteXLSxtableXVector
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 |
