flowTime
Annotation and analysis of biological dynamical systems using flow cytometry
Bioconductor version: Release (3.17)
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>
citation("flowTime")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| Steady-state analysis of flow cytometry data | HTML | R Script |
| Time course analysis of flow cytometry data | HTML | R Script |
| Yeast gating | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, DataImport, FlowCytometry, ImmunoOncology, Software, TimeCourse, Visualization |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (6.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), flowCore |
| Imports | utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang |
| Linking To | |
| Suggests | knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_1.24.0.tar.gz |
| Windows Binary | flowTime_1.24.0.zip |
| macOS Binary (x86_64) | flowTime_1.24.0.tgz |
| macOS Binary (arm64) | flowTime_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/flowTime |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/flowTime |
| Bioc Package Browser | https://code.bioconductor.org/browse/flowTime/ |
| Package Short Url | https://bioconductor.org/packages/flowTime/ |
| Package Downloads Report | Download Stats |