recipe secimtools

Metabolomics tools from the SECIM project



MIT / MIT License



suite of standalone and Galaxy tools for processing of metabolomics data.

package secimtools

(downloads) docker_secimtools



depends bioconductor-impute:

depends lxml:

depends matplotlib-base:

depends matplotlib-venn:

depends numpy:


depends palettable:

depends pandas:

depends perl-vcftools-vcf:

depends pymc:

depends python:


depends r-glmnet:

depends rpy2:

depends scikit-learn:

depends scipy:

depends seaborn:

depends statsmodels:



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 secimtools

and update with::

   mamba update secimtools

To create a new environment, run:

mamba create --name myenvname secimtools

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 `secimtools/tags`_ for valid values for ``<tag>``)

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