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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>

Citation (from within R, enter citation("cyanoFilter")):

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

Details

biocViews Clustering, FlowCytometry, OneChannel, Software
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License MIT + file LICENSE
Depends R (>= 4.1.0)
Imports Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils
Linking To
Suggests magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
System Requirements
Enhances
URL https://github.com/fomotis/cyanoFilter
Bug Reports https://github.com/fomotis/cyanoFilter/issues
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 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