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 released version of tidytof; for the devel version, see tidytof.
Analyze High-dimensional Cytometry Data Using Tidy Data Principles
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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
| Reference Manual |
Details
| biocViews | FlowCytometry, SingleCell, Software |
| Version | 1.6.0 |
| 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 |
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 |