Package: HDStIM
Type: Package
Title: High Dimensional Stimulation Immune Mapping ('HDStIM')
Version: 1.0.0
Authors@R: 
    c(person(given = "Rohit",
             family = "Farmer",
             role = c("aut", "cre"),
             email = "rohit.farmer@gmail.com",
             comment = c(ORCID = "0000-0003-4197-3047")),
      person(given = "Richard",
             family = "Apps",
             role = "aut",
             email = "richard.apps@nih.gov",
             comment = c(ORCID = "0000-0001-5140-0141")),
      person(given = "John",
             family = "Tsang",
             role = c("aut","pdr"),
             email = "john.tsang@nih.gov",
             comment = c(ORCID = "0000-0003-3186-3047")))
Description: A method for identifying responses to experimental
        stimulation in mass or flow cytometry that uses high
        dimensional analysis of measured parameters and can be
        performed with an end-to-end unsupervised approach. In the
        context of in vitro stimulation assays where high-parameter
        cytometry was used to monitor intracellular response markers,
        using cell populations annotated either through automated
        clustering or manual gating for a combined set of stimulated
        and unstimulated samples, 'HDStIM' labels cells as responding
        or non-responding. The package also provides auxiliary
        functions to rank intracellular markers based on their
        contribution to identifying responses and generating diagnostic
        plots.
License: CC0 | file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.2.3
URL: https://github.com/niaid/HDStIM, https://niaid.github.io/HDStIM/
BugReports: https://github.com/niaid/HDStIM/issues
Depends: R (>= 3.6.0)
biocViews: ComplexHeatmap
Imports: tibble, ggplot2, uwot, dplyr, tidyr, magrittr, broom,
        tidyselect, ggridges, Boruta, scales, circlize, ComplexHeatmap
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr, rmarkdown
Language: en-US
Config/pak/sysreqs: libicu-dev libpng-dev perl libclang-dev
Repository: https://niaid.r-universe.dev
Date/Publication: 2023-10-05 20:19:14 UTC
RemoteUrl: https://github.com/niaid/hdstim
RemoteRef: HEAD
RemoteSha: b42e3d83871fe6077362e5a36ab065360a25184e
NeedsCompilation: no
Packaged: 2026-07-04 06:28:49 UTC; root
Author: Rohit Farmer [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4197-3047>),
  Richard Apps [aut] (ORCID: <https://orcid.org/0000-0001-5140-0141>),
  John Tsang [aut, pdr] (ORCID: <https://orcid.org/0000-0003-3186-3047>)
Maintainer: Rohit Farmer <rohit.farmer@gmail.com>