recipe bioconductor-poma

Tools for Omics Data Analysis






A reproducible and easy-to-use toolkit for visualization, pre-processing, exploration, and statistical analysis of omics datasets. The main aim of POMA is to enable a flexible data cleaning and statistical analysis processes in one comprehensible and user-friendly R package. This package has a Shiny app version called POMAShiny that implements all POMA functions. See See Castellano-Escuder P, González-Domínguez R, Carmona-Pontaque F, et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.

package bioconductor-poma

(downloads) docker_bioconductor-poma



depends bioconductor-complexheatmap:


depends bioconductor-deseq2:


depends bioconductor-impute:


depends bioconductor-limma:


depends bioconductor-mixomics:


depends bioconductor-rankprod:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-broom:

depends r-caret:

depends r-dbscan:

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-glasso:


depends r-glmnet:

depends r-magrittr:

depends r-randomforest:

depends r-rmarkdown:

depends r-tibble:

depends r-tidyr:

depends r-uwot:

depends r-vegan:



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-poma

and update with::

   mamba update bioconductor-poma

To create a new environment, run:

mamba create --name myenvname bioconductor-poma

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-poma/tags`_ for valid values for ``<tag>``)

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