Type: Package
Package: tidytof
Title: Analyze High-dimensional Cytometry Data Using Tidy Data Principles
Version: 1.5.0
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
git_url: https://git.bioconductor.org/packages/tidytof
git_branch: devel
git_last_commit: 6312a05
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
