recipe bioconductor-ggcyto

Visualize Cytometry data with ggplot

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ggcyto.html

License:

file LICENSE

Recipe:

/bioconductor-ggcyto/meta.yaml

Links:

biotools: ggcyto, doi: 10.1038/nmeth.3252

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.

package bioconductor-ggcyto

versions:

1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0, 

1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.2-0,  1.10.0-0,  1.8.2-0,  1.6.0-0,  1.4.1-0,  1.4.0-0

depends bioconductor-flowcore:

>=2.14.0,<2.15.0

depends bioconductor-flowworkspace:

>=4.14.0,<4.15.0

depends bioconductor-ncdfflow:

>=2.48.0,<2.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggplot2:

>=3.4.2

depends r-gridextra:

depends r-hexbin:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rlang:

depends r-scales:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-ggcyto

and update with::

   mamba update bioconductor-ggcyto

To create a new environment, run:

mamba create --name myenvname bioconductor-ggcyto

with myenvname being 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-ggcyto:<tag>

(see `bioconductor-ggcyto/tags`_ for valid values for ``<tag>``)

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