recipe bioconductor-flowworkspace

Infrastructure for representing and interacting with gated and ungated cytometry data sets.







biotools: flowworkspace, doi: 10.1186/1471-2105-13-252

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

package bioconductor-flowworkspace

(downloads) docker_bioconductor-flowworkspace



depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-cytolib:


depends bioconductor-delayedarray:


depends bioconductor-flowcore:


depends bioconductor-graph:


depends bioconductor-ncdfflow:


depends bioconductor-rbgl:


depends bioconductor-rgraphviz:


depends bioconductor-rhdf5lib:


depends bioconductor-rprotobuflib:


depends bioconductor-s4vectors:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-bh:


depends r-cpp11:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-matrixstats:

depends r-scales:

depends r-xml:



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-flowworkspace

and update with::

   mamba update bioconductor-flowworkspace

To create a new environment, run:

mamba create --name myenvname bioconductor-flowworkspace

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<tag>

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

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