recipe bioconductor-kmcut

Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/kmcut.html

License:

Artistic-2.0

Recipe:

/bioconductor-kmcut/meta.yaml

The purpose of the package is to identify prognostic biomarkers and an optimal numeric cutoff for each biomarker that can be used to stratify a group of test subjects (samples) into two sub-groups with significantly different survival (better vs. worse). The package was developed for the analysis of gene expression data, such as RNA-seq. However, it can be used with any quantitative variable that has a sufficiently large proportion of unique values.

package bioconductor-kmcut

(downloads) docker_bioconductor-kmcut

versions:

1.0.0-0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-doparallel:

depends r-foreach:

depends r-pracma:

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-kmcut

and update with::

   mamba update bioconductor-kmcut

To create a new environment, run:

mamba create --name myenvname bioconductor-kmcut

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-kmcut:<tag>

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