Package: SuperCell 1.0.1

Leonard Herault

SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells

Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells. 'SuperCell' uses 'velocyto.R' <doi:10.1038/s41586-018-0414-6> <https://github.com/velocyto-team/velocyto.R> for RNA velocity. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.

Authors:Mariia Bilous [aut], Leonard Herault [cre]

SuperCell_1.0.1.tar.gz
SuperCell_1.0.1.tar.gz(r-4.5-noble)SuperCell_1.0.1.tar.gz(r-4.4-noble)
SuperCell_1.0.1.tgz(r-4.4-emscripten)SuperCell_1.0.1.tgz(r-4.3-emscripten)
SuperCell.pdf |SuperCell.html✨
SuperCell/json (API)

# Install 'SuperCell' in R:

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

Bug tracker:https://github.com/gfellerlab/supercell/issues

Datasets:

cell_lines - Cancer cell lines dataset

software

4.18 score 76 scripts 195 downloads 30 exports 141 dependencies

Last updated 5 days agofrom:141ae9293e. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-linux	OK	Oct 26 2024

Exports:anndata_2_supercell build_knn_graph metacell2_anndata_2_supercell sc_mixing_score SCimplify SCimplify_for_velocity SCimplify_from_embedding supercell_2_sce supercell_2_Seurat supercell_assign supercell_cluster supercell_DimPlot supercell_estimate_velocity supercell_FindAllMarkers supercell_FindMarkers supercell_GE supercell_GeneGenePlot supercell_merge supercell_mergeGE supercell_plot supercell_plot_GE supercell_plot_tSNE supercell_plot_UMAP supercell_prcomp supercell_purity supercell_rescale supercell_silhouette supercell_tSNE supercell_UMAP supercell_VlnPlot

Dependencies:askpass backports base64enc bit bit64 boot broom bslib cachem checkmate cli clipr cluster codetools colorspace corpcor cpp11 crayon data.table dbscan digest doFuture dplyr entropy evaluate fansi farver fastcluster fastmap fontawesome forcats foreach foreign Formula fs future future.apply gdata generics ggplot2 glmnet globals glue gridExtra gtable gtools haven here highr Hmisc hms htmlTable htmltools htmlwidgets igraph irlba isoband iterators jomo jquerylib jsonlite knitr labeling lattice lifecycle listenv lme4 magrittr MASS Matrix matrixStats memoise mgcv mice mime minqa mitml munsell nlme nloptr nnet numDeriv openssl ordinal pan parallelly patchwork permute pillar pkgconfig plotfunctions plyr png prettyunits progress progressr proxy purrr R6 RANN rappdirs RColorBrewer Rcpp RcppEigen RcppTOML readr reticulate rlang rmarkdown rpart rprojroot RSpectra rstudioapi Rtsne sass scales shape stringi stringr survival sys tibble tidyr tidyselect tinytex TraMineR tzdb ucminf umap utf8 vctrs vegan vegclust viridis viridisLite vroom WeightedCluster weights withr xfun yaml

Combined or independent SuperCell runs for different samples

Rendered fromb_Combined_vs_independent_sample_processing.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-09-06
Started: 2024-09-06

Example of the SuperCell pipeline

Rendered froma_SuperCell.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-09-06
Started: 2024-09-06

Citation

Readme and manuals

Help Manual

Help page	Topics
Convert Anndata metacell object (Metacell-2 or SEACells) to Super-cell like object	anndata_2_supercell
Build kNN graph	build_knn_graph
Build kNN graph using RANN::nn2 (used in '"build_knn_graph"')	build_knn_graph_nn2
Cancer cell lines dataset	cell_lines
Build kNN graph from distance (used in '"build_knn_graph"')	knn_graph_from_dist
Convert Metacells (Metacell-2) to Super-cell like object	metacell2_anndata_2_supercell
Compute mixing of single-cells within supercell	sc_mixing_score
Detection of metacells with the SuperCell approach	SCimplify
Construct super-cells from spliced and un-spliced matrices	SCimplify_for_velocity
Detection of metacells with the SuperCell approach from low dim representation	SCimplify_from_embedding
Super-cells to SingleCellExperiment object	supercell_2_sce
Super-cells to Seurat object	supercell_2_Seurat
Assign super-cells to the most aboundant cluster	supercell_assign
Cluster super-cell data	supercell_cluster
Plot metacell 2D plot (PCA, UMAP, tSNE etc)	supercell_DimPlot
Run RNAvelocity for super-cells (slightly modified from <https://github.com/velocyto-team/velocyto.R>) Not yet adjusted for super-cell size (not sample-weighted)	supercell_estimate_velocity
Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindAllMarkers (for simplicity)	supercell_FindAllMarkers
Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindMarkers (for simplicity)	supercell_FindMarkers
Simplification of scRNA-seq dataset	supercell_GE
Simplification of scRNA-seq dataset (old version, not used since 12.02.2021)	supercell_GE_idx
Gene-gene correlation plot	supercell_GeneGenePlot
Plot Gene-gene correlation plot for 1 feature	supercell_GeneGenePlot_single
Merging independent SuperCell objects	supercell_merge
Merging metacell gene expression matrices from several independent SuperCell objects	supercell_mergeGE
Plot metacell NW	supercell_plot
Plot super-cell NW colored by an expression of a gene (gradient color)	supercell_plot_GE
Plot super-cell tSNE (Use supercell_DimPlot instead) Plots super-cell tSNE (result of supercell_tSNE)	supercell_plot_tSNE
Plot super-cell UMAP (Use supercell_DimPlot instead) Plots super-cell UMAP (result of supercell_UMAP)	supercell_plot_UMAP
compute PCA for super-cell data (sample-weighted data)	supercell_prcomp
Compute purity of super-cells	supercell_purity
Rescale supercell object	supercell_rescale
Compute Silhouette index accounting for samlpe size (super cells size) ###	supercell_silhouette
Compute tSNE of super-cells	supercell_tSNE
Compute UMAP of super-cells	supercell_UMAP
Violin plots	supercell_VlnPlot
Plot Violin plot for 1 feature	supercell_VlnPlot_single