recipe bioconductor-poma

Tools for Omics Data Analysis

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/POMA.html

License:

GPL-3

Recipe:

/bioconductor-poma/meta.yaml

The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.

package bioconductor-poma

versions:

1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-fgsea:

>=1.32.0,<1.33.0

depends bioconductor-impute:

>=1.80.0,<1.81.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-mixomics:

>=6.30.0,<6.31.0

depends bioconductor-rankprod:

>=3.32.0,<3.33.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-sva:

>=3.54.0,<3.55.0

depends r-base:

>=4.4,<4.5.0a0

depends r-broom:

depends r-caret:

depends r-dbscan:

depends r-dplyr:

depends r-fsa:

depends r-ggcorrplot:

depends r-ggplot2:

depends r-ggrepel:

depends r-glmnet:

depends r-janitor:

depends r-lme4:

depends r-magrittr:

depends r-mass:

depends r-msigdbr:

depends r-multcomp:

depends r-purrr:

depends r-randomforest:

depends r-rlang:

depends r-tibble:

depends r-tidyr:

depends r-uwot:

depends r-vegan:

requirements:

additional platforms:

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-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 quay.io/biocontainers/bioconductor-poma:<tag>

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

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