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.
Version: 0.1.0 Depends: R (≥ 3.6.0) Imports: tibble, ggplot2, uwot, dplyr, tidyr, broom, tidyselect, ggridges, Boruta, scales Suggests: knitr, rmarkdown, testthat Published: 2022-06-24 DOI: 10.32614/CRAN.package.HDStIM Author: Rohit Farmer [aut, cre], Richard Apps [aut], John Tsang [aut, pdr] Maintainer: Rohit Farmer <rohit.farmer at gmail.com> BugReports: https://github.com/niaid/HDStIM/issues License: CC0 | file LICENSE URL: https://github.com/niaid/HDStIM, https://niaid.github.io/HDStIM/ NeedsCompilation: no Language: en-US Materials: README CRAN checks: HDStIM results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=HDStIM to link to this page.
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