Package: staRgate
Title: Automated gating pipeline for flow cytometry analysis to
        characterize the lineage, differentiation, and functional
        states of T-cells
Version: 1.0.0
Authors@R: 
    c(
    person("Jasme", "Lee", email = "leej22@mskcc.org", role = c("aut", "cre"),
           comment = c(ORCID = "0009-0006-4492-4872")),
    person("Matthew", "Adamow", role = c("aut")),
    person("Colleen", "Maher", role = c("aut")),
    person("Xiyu", "Peng", role = c("aut")),
    person("Phillip", "Wong", role = c("aut")),
    person("Fiona", "Ehrich", role = c("aut")),
    person("Michael", "Postow", middle = "A", role = c("aut")),
    person("Margaret", "Callahan", middle = "K", role = c("aut")),
    person("Ronglai", "Shen", role = c("aut")),
    person("Katherine", "Panageas", middle = "S", role = c("aut")),
    person("V foundation", role = "fnd"),
    person("MSK-MIND", role = "fnd"),
    person("NIH R01CA276286", role = "fnd"),
    person("NIH P30CA008748", role = "fnd")
    )
Description: An R-based automated gating pipeline for flow cytometry
        data designed to mimic the manual gating strategy of defining
        flow biomarker positive populations relative to a unimodal
        background population to include cells with varying intensities
        of marker expression. The pipeline’s main feature is a flexible
        density-based gating strategy capable of capturing varying
        scenarios based on marker expression patterns to analyze a
        29-marker flow panel that characterizes T-cell lineage,
        differentiation, and functional states.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
biocViews: FlowCytometry, Preprocessing, ImmunoOncology
Depends: R (>= 4.3.0)
Imports: dplyr, janitor, purrr, rlang, stringr, tidyr, flowCore,
        flowWorkspace, glue, tibble
Suggests: flowAI, ggplot2, gt, knitr, openCyto, ggcyto, rmarkdown,
        data.table, here, testthat (>= 3.0.0), BiocStyle
VignetteBuilder: knitr
BugReports: https://github.com/leejasme/staRgate/issues
URL: https://bioconductor.org/packages/staRgate,
        https://leejasme.github.io/staRgate
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:06:10 UTC
RemoteUrl: https://github.com/bioc/staRgate
RemoteRef: RELEASE_3_23
RemoteSha: 2bcb2c931f87a820f92a4806b55f14a4207053e5
NeedsCompilation: no
Packaged: 2026-04-30 06:44:58 UTC; root
Author: Jasme Lee [aut, cre] (ORCID: <https://orcid.org/0009-0006-4492-4872>),
  Matthew Adamow [aut],
  Colleen Maher [aut],
  Xiyu Peng [aut],
  Phillip Wong [aut],
  Fiona Ehrich [aut],
  Michael A Postow [aut],
  Margaret K Callahan [aut],
  Ronglai Shen [aut],
  Katherine S Panageas [aut],
  V foundation [fnd],
  MSK-MIND [fnd],
  NIH R01CA276286 [fnd],
  NIH P30CA008748 [fnd]
Maintainer: Jasme Lee <leej22@mskcc.org>
Built: R 4.6.0; ; 2026-04-30 07:54:35 UTC; unix
