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Bioconductor - tidytof (development version)

tidytof

This is the development version of tidytof; for the stable release version, see tidytof.

Analyze High-dimensional Cytometry Data Using Tidy Data Principles

Bioconductor version: Development (3.22)

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.

Author: Timothy Keyes [cre] ORCID: 0000-0003-0423-9679 , Kara Davis [rth, own], Garry Nolan [rth, own]

Maintainer: Timothy Keyes <tkeyes at stanford.edu>

Citation (from within R, enter citation("tidytof")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("tidytof")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tidytof")

Details biocViews FlowCytometry, SingleCell, Software Version 1.3.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) 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 System Requirements URL https://keyes-timothy.github.io/tidytof https://keyes-timothy.github.io/tidytof/ Bug Reports https://github.com/keyes-timothy/tidytof/issues See More 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 Linking To Rcpp Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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