Package Recipe 'bioconductor-clustall'

recipe bioconductor-clustall

ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/ClustAll.html
License:: GPL-2
Recipe:: /bioconductor-clustall/meta.yaml

Data driven strategy to find hidden groups of patients with complex diseases using clinical data. ClustAll facilitates the unsupervised identification of multiple robust stratifications. ClustAll, is able to overcome the most common limitations found when dealing with clinical data (missing values, correlated data, mixed data types).

package bioconductor-clustall¶

Versions:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-complexheatmap >=2.26.0,<2.27.0
on r-base >=4.5,<4.6.0a0
on r-bigstatsr
on r-circlize
on r-cluster
on r-clvalid
on r-dosnow
on r-dplyr
on r-factominer
on r-flock
on r-foreach
on r-fpc
on r-ggplot2
on r-mice
on r-modeest
on r-networkd3
on r-pbapply
on r-rcolorbrewer

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-clustall

to add into an existing workspace instead, run:

pixi add bioconductor-clustall

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-clustall

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-clustall

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-clustall:<tag>

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