Package: CSOA
Type: Package
Title: Calculate per-cell gene signature scores in scRNA-seq data using
        cell set overlaps
Version: 1.1.5
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: bayesbio, 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: libfontconfig1-dev libfreetype6-dev libglpk-dev
        make libicu-dev libpng-dev libxml2-dev libssl-dev python3
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-03-19 02:00:13 UTC
RemoteUrl: https://github.com/bioc/CSOA
RemoteRef: HEAD
RemoteSha: fe3c38cb539374005aab2110b9597a03d1b2207b
NeedsCompilation: no
Packaged: 2026-03-19 06:09:22 UTC; root
Author: Andrei-Florian Stoica [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5253-0826>)
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Built: R 4.6.0; ; 2026-03-19 06:13:12 UTC; windows
