HDStIM: High Dimensional Stimulation Immune Mapping ('HDStIM') (original) (raw)
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 |
| URL: | https://github.com/niaid/HDStIM, https://niaid.github.io/HDStIM/ |
| NeedsCompilation: | no |
| Language: | en-US |
| Materials: | README |
| CRAN checks: | HDStIM results |
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