recipe bioconductor-sigsquared

Gene signature generation for functionally validated signaling pathways

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/sigsquared.html

License:

GPL version 3

Recipe:

/bioconductor-sigsquared/meta.yaml

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

versions:
1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0, 

1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-survival:

requirements:

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

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-sigsquared/README.html)