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cyanoFilter

This is the development version of cyanoFilter; for the stable release version, see cyanoFilter.

Phytoplankton Population Identification using Cell Pigmentation and/or Complexity


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1.0)
Imports Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils
System Requirements
URL https://github.com/fomotis/cyanoFilter
Bug Reports https://github.com/fomotis/cyanoFilter/issues
See More
Suggests magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
Linking To
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Depends On Me
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Suggests Me
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Package Archives

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

Source Package cyanoFilter_1.11.0.tar.gz
Windows Binary cyanoFilter_1.11.0.zip
macOS Binary (x86_64) cyanoFilter_1.11.0.tgz
macOS Binary (arm64) cyanoFilter_1.11.0.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