flowTime

DOI: 10.18129/B9.bioc.flowTime    

Annotation and analysis of biological dynamical systems using flow cytometry

Bioconductor version: Release (3.13)

This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.

Author: R. Clay Wright [aut, cre], Nick Bolten [aut], Edith Pierre-Jerome [aut]

Maintainer: R. Clay Wright <wright.clay at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("flowTime")

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("flowTime")

 

HTML	R Script	Steady-state analysis of flow cytometry data
HTML	R Script	Time course analysis of flow cytometry data
HTML	R Script	Yeast gating
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, DataImport, FlowCytometry, ImmunoOncology, Software, TimeCourse, Visualization
Version	1.16.1
In Bioconductor since	BioC 3.5 (R-3.4) (4.5 years)
License	Artistic-2.0
Depends	R (>= 3.4), flowCore
Imports	utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang
LinkingTo
Suggests	knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	flowTime_1.16.1.tar.gz
Windows Binary	flowTime_1.16.1.zip
macOS 10.13 (High Sierra)	flowTime_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/flowTime
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/flowTime
Package Short Url	https://bioconductor.org/packages/flowTime/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive