Package: CSOA 1.2.0

Andrei-Florian Stoica

CSOA: Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps

Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in an scRNA-seq dataset. CSOA constructs a set for each gene in the signature, consisting of the cells that highly express the gene. Next, all overlaps of pairs of cell sets are computed, ranked, filtered and scored. The CSOA per-cell score is calculated by summing up all products of the overlap scores and the min-max-normalized expression of the two involved genes. CSOA can run on a Seurat object, a SingleCellExperiment object, a matrix and a dgCMatrix.

Authors:Andrei-Florian Stoica [aut, cre]

CSOA_1.2.0.tar.gz
CSOA_1.2.0.zip(r-4.7-any)CSOA_1.2.0.zip(r-4.6-any)CSOA_1.2.0.zip(r-4.5-any)
CSOA_1.2.0.tgz(r-4.6-any)CSOA_1.2.0.tgz(r-4.5-any)
CSOA_1.2.0.tar.gz(r-4.7-any)CSOA_1.2.0.tar.gz(r-4.6-any)
CSOA_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CSOA/json (API)

# Install 'CSOA' in R:

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

Bug tracker:https://github.com/andrei-stoica26/csoa/issues

On BioConductor:CSOA-1.3.3(bioc 3.24)CSOA-1.2.0(bioc 3.23)

software singlecell genesetenrichment geneexpression

6.10 score 4 stars 1 packages 5 scripts 241 downloads 20 exports 181 dependencies

Last updated from:c99f3964a3 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	361
linux-devel	OK	522
source / vignettes	OK	473
linux-release	OK	485
macos-release	OK	406
macos-oldrel	OK	386
windows-devel	OK	1197
windows-release	OK	1217
windows-oldrel	OK	1628
wasm-release	OK	197

Exports:attachCellScores basicHeatmap breakWeakTies cellDistribution cellSetsOverlaps expMat featureWes geneRadialPlot generateOverlaps getPairs overlapCutoffPlot overlapGenes overlapNetworkPlot overlapPairs percentileSets processOverlaps qGrab runCSOA scoreCells scoreModules

Dependencies:abdiv abind ape askpass base64enc BH Biobase BiocGenerics bitops bslib cachem caTools class cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics GenomicRanges ggalluvial ggeasy ggforce ggnewscale ggplot2 ggraph ggrepel ggridges globals glue goftest gplots graphlayouts gridExtra gtable gtools henna here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite kernlab KernSmooth kerntools knitr labeling later lattice lazyeval lifecycle listenv liver lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel paletteer parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip prismatic progressr promises purrr qs2 R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppParallel RcppProgress RcppThread RcppTOML rematch2 reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra rstudioapi Rtsne S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject shiny sitmo slam sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringfish stringi stringr SummarizedExperiment survival sys systemfonts tensor textshape tibble tidygraph tidyr tidyselect tinytex tweenr utf8 uwot vctrs viridis viridisLite withr xfun xtable XVector yaml zoo

The CSOA algorithm

Rendered fromThe-CSOA-algorithm.Rmdusingknitr::rmarkdown

Last update: 2026-04-17
Started: 2025-08-13

Advanced CSOA

Rendered fromAdvanced-CSOA.Rmdusingknitr::rmarkdown

Last update: 2026-03-11
Started: 2025-08-13

CSOA

Introduction | Installation | Prerequisites | Scoring gene sets | Session information

Rendered fromCSOA.Rmdusingknitr::rmarkdown

Last update: 2025-10-22
Started: 2025-06-06

Help page	Topics
Attach CSOA scores to object	attachCellScores attachCellScores.default attachCellScores.dgCMatrix attachCellScores.matrix attachCellScores.Seurat attachCellScores.SingleCellExperiment
Plot a simple heatmap	basicHeatmap
Remove overlap pairs with low Jaccard scores	breakWeakTies
Show the distribution of cell sets among cells	cellDistribution
Calculates the significance of overlaps of pairs of cells sets	cellSetsOverlaps
Extracts the data expression matrix from object	expMat expMat.default expMat.dgCMatrix expMat.matrix expMat.Seurat expMat.SingleCellExperiment
A feature plot with a more distinctive color scheme.	featureWes
Radial plot for an overlap data frame	geneRadialPlot
Generate overlaps of cell sets for input genes	generateOverlaps
Get all unordered pairs of two elements from a vector	getPairs
Plot the selection of overlaps	overlapCutoffPlot
Get all genes from an overlap data frame	overlapGenes
Plot the overlaps as a network	overlapNetworkPlot
Extract gene pairs from overlap data frame	overlapPairs
Generates cell expressing input genes at an input percentile	percentileSets
Process data frame of overlaps of cell sets	processOverlaps
Read and delete a .qs2 file	qGrab
Run the CSOA pipeline	runCSOA
Generate CSOA scores from overlap data frame and list of pairs	scoreCells
Run CSOA separately on the connected components of the overlap graph	scoreModules

Package: CSOA 1.2.0

CSOA: Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)