tidytof

Analyze High-dimensional Cytometry Data Using Tidy Data Principles


Bioconductor version: Release (3.20)

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

Installation

To install this package, start R (version "4.4") and enter:


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

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")
01. Getting started with tidytof HTML R Script
02. Reading and writing data HTML R Script
03. Quality control HTML R Script
04. Preprocessing HTML R Script
05. Downsampling HTML R Script
06. Dimensionality reduction HTML R Script
07. Clustering and metaclustering HTML R Script
08. Differential discovery analysis HTML R Script
09. Feature extraction HTML R Script
10. Modeling HTML R Script
11. How to contribute code HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews FlowCytometry, SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)
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.

Source Package tidytof_1.0.0.tar.gz
Windows Binary (x86_64) tidytof_1.0.0.zip (64-bit only)
macOS Binary (x86_64) tidytof_1.0.0.tgz
macOS Binary (arm64) tidytof_0.99.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/tidytof
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tidytof
Bioc Package Browser https://code.bioconductor.org/browse/tidytof/
Package Short Url https://bioconductor.org/packages/tidytof/
Package Downloads Report Download Stats