recipe bioconductor-sigcheck

Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-sigcheck/meta.yaml

While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.

package bioconductor-sigcheck

(downloads) docker_bioconductor-sigcheck

versions:
2.34.0-0,  2.32.0-0,  2.30.0-0,  2.26.0-0,  2.24.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0, 

2.34.0-0,  2.32.0-0,  2.30.0-0,  2.26.0-0,  2.24.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-mlinterfaces:

>=1.82.0,<1.83.0

depends r-base:

>=4.3,<4.4.0a0

depends r-e1071:

depends r-survival:

requirements:

additional platforms:

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-sigcheck

and update with::

   mamba update bioconductor-sigcheck

To create a new environment, run:

mamba create --name myenvname bioconductor-sigcheck

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-sigcheck:<tag>

(see `bioconductor-sigcheck/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-sigcheck/README.html)