recipe bioconductor-safe

Significance Analysis of Function and Expression



GPL (>= 2)




biotools: safe, doi: 10.1093/bioinformatics/bti260

SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.

package bioconductor-safe

(downloads) docker_bioconductor-safe



depends bioconductor-annotationdbi:


depends bioconductor-biobase:


depends r-base:


depends r-sparsem:



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-safe

and update with::

   mamba update bioconductor-safe

To create a new environment, run:

mamba create --name myenvname bioconductor-safe

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

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