recipe bioconductor-opencyto

Hierarchical Gating Pipeline for flow cytometry data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/openCyto.html

License:

AGPL-3.0-only

Recipe:

/bioconductor-opencyto/meta.yaml

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

package bioconductor-opencyto

(downloads) docker_bioconductor-opencyto

versions:
2.12.0-02.10.0-12.10.0-02.6.0-22.6.0-12.6.0-02.4.0-02.2.0-22.2.0-1

2.12.0-02.10.0-12.10.0-02.6.0-22.6.0-12.6.0-02.4.0-02.2.0-22.2.0-12.2.0-02.0.0-01.24.0-01.22.2-01.20.1-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-flowclust:

>=3.38.0,<3.39.0

depends bioconductor-flowcore:

>=2.12.0,<2.13.0

depends bioconductor-flowviz:

>=1.64.0,<1.65.0

depends bioconductor-flowworkspace:

>=4.12.0,<4.13.0

depends bioconductor-graph:

>=1.78.0,<1.79.0

depends bioconductor-ncdfflow:

>=2.46.0,<2.47.0

depends bioconductor-rbgl:

>=1.76.0,<1.77.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

depends r-cpp11:

depends r-data.table:

depends r-rcolorbrewer:

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-opencyto

and update with::

   mamba update bioconductor-opencyto

To create a new environment, run:

mamba create --name myenvname bioconductor-opencyto

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-opencyto:<tag>

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

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