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("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 | ||
| 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 |
| 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 |