recipe bioconductor-metapone

Conducts pathway test of metabolomics data using a weighted permutation test






The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.

package bioconductor-metapone

(downloads) docker_bioconductor-metapone



depends bioconductor-biocparallel:


depends bioconductor-fgsea:


depends r-base:


depends r-fdrtool:

depends r-fields:

depends r-ggplot2:

depends r-ggrepel:

depends r-markdown:



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-metapone

and update with::

   mamba update bioconductor-metapone

To create a new environment, run:

mamba create --name myenvname bioconductor-metapone

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

Download stats