- recipe bioconductor-cyanofilter
Phytoplankton Population Identification using Cell Pigmentation and/or Complexity
MIT + file LICENSE
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.
- package bioconductor-cyanofilter¶
- depends bioconductor-biobase:
- depends bioconductor-flowclust:
- depends bioconductor-flowcore:
- depends bioconductor-flowdensity:
- depends r-base:
- depends r-cytometree:
- depends r-ggally:
- depends r-ggplot2:
- depends r-mrfdepth:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-cyanofilter and update with:: mamba update bioconductor-cyanofilter
To create a new environment, run:
mamba create --name myenvname bioconductor-cyanofilter
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-cyanofilter:<tag> (see `bioconductor-cyanofilter/tags`_ for valid values for ``<tag>``)