Bioconductor - cyanoFilter
Bioconductor 3.22
Software Packages
cyanoFilter
cyanoFilter
This is the
released
version of cyanoFilter; for the devel version, see
cyanoFilter
Phytoplankton Population Identification using Cell Pigmentation and/or Complexity
DOI:
10.18129/B9.bioc.cyanoFilter
Bioconductor version:
Release (3.22)
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
Citation (from within R, enter
citation("cyanoFilter")
):
Installation
To install this package, start R (version "4.5") 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
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Details
biocViews
Clustering
FlowCytometry
OneChannel
Software
Version
1.18.0
In Bioconductor since
BioC 3.13 (R-4.1) (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
System Requirements
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magrittr
dplyr
purrr
knitr
stringr
rmarkdown
tidyr
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instructions to use this package in your R session.
Source Package
cyanoFilter_1.18.0.tar.gz
Windows Binary (x86_64)
cyanoFilter_1.18.0.zip
(64-bit only)
macOS Binary (x86_64)
cyanoFilter_1.18.0.tgz
macOS Binary (arm64)
cyanoFilter_1.18.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/cyanoFilter
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/cyanoFilter
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