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HDStIM: High Dimensional Stimulation Immune Mapping ('HDStIM')
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:
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.