Package Recipe 'bioconductor-cpsm'

recipe bioconductor-cpsm

CPSM: Cancer patient survival model

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/CPSM.html
License:: GPL-3 | file LICENSE
Recipe:: /bioconductor-cpsm/meta.yaml

CPSM provides a comprehensive computational pipeline for predicting survival probability and risk groups in cancer patients. The package includes steps for data preprocessing, training/test split, and normalization. It enables feature selection using univariate survival analysis and computes a LASSO-based prognostic index (PI) score. CPSM supports the development of predictive models using various feature sets and offers a suite of visualization tools, including survival curves based on predicted probabilities, barplots for predicted mean and median survival times, KM plots overlaid with individual survival predictions, and nomograms for estimating 1-, 3-, 5-, and 10-year survival probabilities. This makes CPSM a versatile tool for survival analysis in cancer research.

package bioconductor-cpsm¶

Versions:

1.2.0-0

Depends:

on bioconductor-preprocesscore >=1.72.0,<1.73.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-caret
on r-ggfortify
on r-ggplot2
on r-glmnet
on r-hmisc
on r-mass
on r-matrix
on r-mtlr
on r-randomforestsrc
on r-reshape2
on r-rms
on r-survival
on r-survmetrics
on r-survminer

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-cpsm

to add into an existing workspace instead, run:

pixi add bioconductor-cpsm

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-cpsm

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cpsm

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-cpsm:<tag>

(see bioconductor-cpsm/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-cpsm/README.html)