Package: CSOA
Type: Package
Title: Calculate per-cell gene signature scores in scRNA-seq data using
        cell set overlaps
Version: 0.99.3
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, qs,
        reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment,
        sgof, spatstat.utils, stats, textshape, wesanderson
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
git_url: https://git.bioconductor.org/packages/CSOA
git_branch: devel
git_last_commit: e6c6678
git_last_commit_date: 2025-10-22
Repository: Bioconductor 3.22
Date/Publication: 2025-10-23
NeedsCompilation: no
Packaged: 2025-10-23 20:05:33 UTC; biocbuild
Author: Andrei-Florian Stoica [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5253-0826>)
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Built: R 4.5.1; ; 2025-10-24 03:06:01 UTC; unix
