tidytof
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
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 (3.24)
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] 
, Kara Davis [rth, own], Garry Nolan [rth, own]
Maintainer: Timothy Keyes <tkeyes at stanford.edu>
citation("tidytof")):Timothy Keyes, Kara Davis, Garry Nolan. tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles. doi:10.18129/B9.bioc.tidytof, R package version 1.7.0, https://bioconductor.org/packages/tidytof.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("tidytof")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| No vignettes available | |
| Reference Manual |
Details
| biocViews | FlowCytometry, SingleCell, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/tidytof |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidytof |
| Package Short Url | https://bioconductor.org/packages/tidytof/ |
| Package Downloads Report | Download Stats |