cyanoFilter

DOI: 10.18129/B9.bioc.cyanoFilter  

Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

Bioconductor version: Release (3.17)

An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.

Author: Oluwafemi Olusoji [cre, aut], Aerts Marc [ctb], Delaender Frederik [ctb], Neyens Thomas [ctb], Spaak jurg [aut]

Maintainer: Oluwafemi Olusoji <oluwafemi.olusoji at uhasselt.be>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("cyanoFilter")

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("cyanoFilter")

 

HTML	R Script	cyanoFilter: A Semi-Automated Framework for Identifying Phytplanktons and Cyanobacteria Population in Flow Cytometry
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, FlowCytometry, OneChannel, Software
Version	1.8.0
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils
LinkingTo
Suggests	magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
SystemRequirements
Enhances
URL	https://github.com/fomotis/cyanoFilter
BugReports	https://github.com/fomotis/cyanoFilter/issues
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	cyanoFilter_1.8.0.tar.gz
Windows Binary	cyanoFilter_1.8.0.zip
macOS Binary (x86_64)	cyanoFilter_1.8.0.tgz
macOS Binary (arm64)	cyanoFilter_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cyanoFilter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cyanoFilter
Bioc Package Browser	https://code.bioconductor.org/browse/cyanoFilter/
Package Short Url	https://bioconductor.org/packages/cyanoFilter/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive