Package: scaper
Title: Single Cell Transcriptomics-Level Cytokine Activity Prediction
        and Estimation
Version: 0.2.1
Authors@R: c(
    person("Zaoqu", "Liu", email = "liuzaoqu@163.com", role = c("aut", "cre")),
    person("H. Robert", "Frost", email = "hildreth.r.frost@dartmouth.edu", role = c("aut")),
    person("Azka", "Javaid", email = "azka.javaid.gr@dartmouth.edu", role = c("aut")))
Maintainer: Zaoqu Liu <liuzaoqu@163.com>
URL: https://github.com/Zaoqu-Liu/scaper
BugReports: https://github.com/Zaoqu-Liu/scaper/issues
Description: Generates cell-level cytokine activity estimates using
        relevant information from gene sets constructed with the
        'CytoSig' and the 'Reactome' databases and scored using the
        modified 'Variance-adjusted Mahalanobis (VAM)' framework for
        single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database
        is described in: Jiang at al., (2021)
        <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is
        described in: Gillespie et al., (2021)
        <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in:
        Frost (2020) <doi:10.1093/nar/gkaa582>.
Suggests: knitr, pheatmap, rmarkdown, usethis
Imports: magrittr, xml2, stringr, dplyr, Seurat, SeuratObject, MASS,
        Matrix, methods, utils
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2026-07-05 05:02:54 UTC; root
Author: Zaoqu Liu [aut, cre], H. Robert Frost [aut], Azka Javaid [aut]
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-25 17:24:59 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/scaper
RemoteRef: main
RemoteSha: 76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5