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
Author: Rohit Farmer ORCID iD [aut, cre], Richard Apps ORCID iD [aut], John Tsang ORCID iD [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:

Reference manual: HDStIM.pdf
Vignettes: HDStIM

Downloads:

Package source: HDStIM_0.1.0.tar.gz
Windows binaries: r-devel: HDStIM_0.1.0.zip, r-release: HDStIM_0.1.0.zip, r-oldrel: HDStIM_0.1.0.zip
macOS binaries: r-release (arm64): HDStIM_0.1.0.tgz, r-oldrel (arm64): HDStIM_0.1.0.tgz, r-release (x86_64): HDStIM_0.1.0.tgz

Linking:

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