DESCRIPTION

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