flowTime

DOI: 10.18129/B9.bioc.flowTime    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see flowTime.

Annotation and analysis of biological dynamical systems using flow cytometry

Bioconductor version: 3.7

This package was developed for analysis of both dynamic and steady state experiments examining the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using a 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 is requisite for dissemination and general ease-of-use. 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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flowTime")

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
PDF		Reference Manual

Details

biocViews	CellBasedAssays, DataImport, FlowCytometry, Software, TimeCourse, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.5 (R-3.4) (1.5 years)
License	Artistic-2.0
Depends	R (>= 3.4), flowCore, plyr
Imports	utils
LinkingTo
Suggests	knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments, stats
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_1.4.0.tar.gz
Windows Binary	flowTime_1.4.0.zip
Mac OS X 10.11 (El Capitan)	flowTime_1.4.0.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	http://bioconductor.org/packages/flowTime/
Package Downloads Report	Download Stats