recipe bioconductor-sigsquared

Gene signature generation for functionally validated signaling pathways



GPL version 3



By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.

package bioconductor-sigsquared

(downloads) docker_bioconductor-sigsquared



depends bioconductor-biobase:


depends r-base:


depends r-survival:



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-sigsquared

and update with::

   mamba update bioconductor-sigsquared

To create a new environment, run:

mamba create --name myenvname bioconductor-sigsquared

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

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