Package Recipe 'bioconductor-sigcheck'

recipe bioconductor-sigcheck

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

Homepage:: https://bioconductor.org/packages/3.20/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¶

Versions:

2.42.0-0, 2.38.0-0, 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,

2.42.0-0, 2.38.0-0, 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:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-mlinterfaces >=1.90.0,<1.91.0
on r-base >=4.5,<4.6.0a0
on r-e1071
on r-survival

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-sigcheck

to add into an existing workspace instead, run:

pixi add bioconductor-sigcheck

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-sigcheck

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-sigcheck

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-sigcheck:<tag>

(see bioconductor-sigcheck/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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)