Type: Package
Package: SPAROscore
Title: A package to compute gene signature scores from transcriptomics
        data
Version: 0.99.3
Authors@R: 
    person("Venkatesh", "Kamaraj", , "venkatesh.kamaraj@adelaide.edu.au", role = c("aut", "cre"),
           comment = c(ORCID = "0009-0008-7309-9810"))
Description: SPAROscore is a gene signature scoring method designed to
        be robust across diverse gene expression datasets. SPAROscore
        adapts to varying levels of sparsity, allowing signature scores
        to be efficiently computed across bulk, single-cell, and
        spatial transcriptomic datasets.  The resulting scores quantify
        the relative expression of a gene signature compared with the
        background expression of each sample/cell/domain, making the
        scores straightforward to interpret biologically.  Internally,
        SPAROscore ranks genes within each column and computes the
        Spearman footrule distance between the observed ranks of the
        signature genes and a background gene expression rank estimated
        from the geometric mean expression of the sample, cell, or
        spatial domain.
License: GPL-3
URL: https://github.com/MangiolaLaboratory/SPAROscore
BugReports: https://github.com/MangiolaLaboratory/SPAROscore/issues
Imports: DelayedArray, DelayedMatrixStats, Matrix, MatrixGenerics,
        matrixStats, methods, sparseMatrixStats, stats
Suggests: airway, dplyr, edgeR, ggplot2, ggspavis, GSEABase, knitr,
        msigdbr, muscData, rmarkdown, scater, Seurat,
        SingleCellExperiment, SpatialExperiment, spatialLIBD,
        SummarizedExperiment, testthat (>= 3.0.0), tidyr
VignetteBuilder: knitr
biocViews: GeneExpression, SingleCell, Spatial, Transcriptomics,
        GeneSetEnrichment, Pathways, Software
Config/testthat/edition: 3
Encoding: UTF-8
RoxygenNote: 7.3.3
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-07-22 06:33:11 UTC
RemoteUrl: https://github.com/BiocStaging/SPAROscore
RemoteRef: HEAD
RemoteSha: bb23f80ef8e9fca0dd1d3e8362a266d8dd2a0af6
NeedsCompilation: no
Packaged: 2026-07-22 08:07:58 UTC; root
Author: Venkatesh Kamaraj [aut, cre] (ORCID:
    <https://orcid.org/0009-0008-7309-9810>)
Maintainer: Venkatesh Kamaraj <venkatesh.kamaraj@adelaide.edu.au>