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 (3.24)
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("cyanoFilter")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, FlowCytometry, OneChannel, Software |
| Version | 1.21.0 |
| 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 | |
| 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 | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cyanoFilter_1.21.0.tar.gz |
| Windows Binary (x86_64) | cyanoFilter_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | cyanoFilter_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | cyanoFilter_1.21.0.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 |