Type: Package
Package: tidytof
Title: Analyze High-dimensional Cytometry Data Using Tidy Data
        Principles
Version: 1.6.0
Authors@R: 
    c(person(given = "Timothy",
             family = "Keyes",
             role = c("cre"),
             email = "tkeyes@stanford.edu", 
             comment = c(ORCID = "0000-0003-0423-9679")),
      person(given = "Kara", 
             family = "Davis", 
             role = c("rth", "own"),
             email = "kldavis@stanford.edu"), 
      person(given = "Garry", 
             family = "Nolan", 
             role = c("rth", "own"), 
             email = "gnolan@stanford.edu"))    
Description: This package implements an interactive, scientific
        analysis pipeline for high-dimensional cytometry data built
        using tidy data principles. It is specifically designed to play
        well with both the tidyverse and Bioconductor software
        ecosystems, with functionality for reading/writing data files,
        data cleaning, preprocessing, clustering, visualization,
        modeling, and other quality-of-life functions. tidytof
        implements a "grammar" of high-dimensional cytometry data
        analysis.
License: MIT + file LICENSE
Depends: R (>= 4.3)
Imports: doParallel, dplyr, flowCore, foreach, ggplot2, ggraph, glmnet,
        methods, parallel, purrr, readr, recipes, rlang, stringr,
        survival, tidygraph, tidyr, tidyselect, yardstick, Rcpp,
        tibble, stats, utils, RcppHNSW
Suggests: ConsensusClusterPlus, Biobase, broom, covr, diffcyt, emdist,
        FlowSOM, forcats, ggrepel, HDCytoData, knitr, markdown,
        philentropy, rmarkdown, Rtsne, statmod, SummarizedExperiment,
        testthat (>= 3.0.0), lmerTest, lme4, ggridges, spelling,
        scattermore, preprocessCore, SingleCellExperiment, Seurat,
        SeuratObject, embed, rsample, BiocGenerics
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.1
LinkingTo: Rcpp
URL: https://keyes-timothy.github.io/tidytof,
        https://keyes-timothy.github.io/tidytof/
BugReports: https://github.com/keyes-timothy/tidytof/issues
VignetteBuilder: knitr
Language: en-US
biocViews: SingleCell, FlowCytometry
PackageStatus: Deprecated
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        libicu-dev libxml2-dev libssl-dev libx11-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 13:03:36 UTC
RemoteUrl: https://github.com/bioc/tidytof
RemoteRef: RELEASE_3_23
RemoteSha: 8e9516428ac396d26fbc043b41444ebce4f1129d
NeedsCompilation: yes
Packaged: 2026-07-04 15:31:41 UTC; root
Author: Timothy Keyes [cre] (ORCID: <https://orcid.org/0000-0003-0423-9679>),
  Kara Davis [rth, own],
  Garry Nolan [rth, own]
Maintainer: Timothy Keyes <tkeyes@stanford.edu>