Package: CSOA Type: Package Title: Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps Version: 1.3.1 Authors@R: person('Andrei-Florian', 'Stoica', email='andreistoica@foxmail.com', role=c('aut','cre'), comment=c(ORCID='0000-0002-5253-0826')) Description: 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. License: MIT + file LICENSE Imports: dplyr, ggplot2, henna, kerntools, methods, paletteer, qs2, reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment, spatstat.utils, stats, textshape Encoding: UTF-8 RoxygenNote: 7.3.3 Suggests: BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle, stringr, testthat (>= 3.0.0) biocViews: Software, SingleCell, GeneSetEnrichment, GeneExpression VignetteBuilder: knitr URL: https://github.com/andrei-stoica26/CSOA BugReports: https://github.com/andrei-stoica26/CSOA/issues Config/testthat/edition: 3 Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-05-06 06:48:28 UTC RemoteUrl: https://github.com/bioc/CSOA RemoteRef: HEAD RemoteSha: 959ac2950f251e44bab4c286a51195b086243236 NeedsCompilation: no Packaged: 2026-06-05 06:27:33 UTC; root Author: Andrei-Florian Stoica [aut, cre] (ORCID: ) Maintainer: Andrei-Florian Stoica