Package Recipe 'bioconductor-rcm'

recipe bioconductor-rcm

Fit row-column association models with the negative binomial distribution for the microbiome

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

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

package bioconductor-rcm¶

Versions:

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0,

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-1

Depends:

on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-phyloseq >=1.54.0,<1.55.0
on r-alabama
on r-base >=4.5,<4.6.0a0
on r-ggplot2 >=2.2.1.9000
on r-mass
on r-nleqslv
on r-rcolorbrewer
on r-reshape2
on r-tensor
on r-tseries
on r-vgam

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-rcm

to add into an existing workspace instead, run:

pixi add bioconductor-rcm

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-rcm

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rcm

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-rcm:<tag>

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