Package Recipe 'bioconductor-classifyr'

recipe bioconductor-classifyr

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/ClassifyR.html
License:: GPL-3
Recipe:: /bioconductor-classifyr/meta.yaml
Links:: biotools: classifyr

The software formalises a framework for classification and survival model evaluation in R. There are four stages; Data transformation, feature selection, model training, and prediction. The requirements of variable types and variable order are fixed, but specialised variables for functions can also be provided. The framework is wrapped in a driver loop that reproducibly carries out a number of cross-validation schemes. Functions for differential mean, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.

package bioconductor-classifyr¶

Versions:

3.14.0-0, 3.10.0-0, 3.6.2-0, 3.4.7-1, 3.4.7-0, 3.2.0-1, 3.2.0-0, 2.14.0-0, 2.12.0-0,

3.14.0-0, 3.10.0-0, 3.6.2-0, 3.4.7-1, 3.4.7-0, 3.2.0-1, 3.2.0-0, 2.14.0-0, 2.12.0-0, 2.10.0-1, 2.10.0-0, 2.8.0-0, 2.6.0-0, 2.4.4-0, 2.2.6-0, 2.2.4-0, 2.0.10-0, 1.12.2-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-dcanr >=1.26.0,<1.27.0
on bioconductor-dcanr >=1.26.0,<1.27.0a0
on bioconductor-genefilter >=1.92.0,<1.93.0
on bioconductor-genefilter >=1.92.0,<1.93.0a0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-multiassayexperiment >=1.36.1,<1.37.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-broom
on r-dplyr
on r-generics
on r-ggplot2 >=3.5.0
on r-ggpubr
on r-ggupset
on r-ranger
on r-reshape2
on r-rlang
on r-survival
on r-tidyr

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-classifyr

to add into an existing workspace instead, run:

pixi add bioconductor-classifyr

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-classifyr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-classifyr

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-classifyr:<tag>

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