Package Recipe 'bioconductor-mbecs'

recipe bioconductor-mbecs

Evaluation and correction of batch effects in microbiome data-sets

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/MBECS.html
License:: Artistic-2.0
Recipe:: /bioconductor-mbecs/meta.yaml

The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

package bioconductor-mbecs¶

Versions:

1.14.0-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-0

Depends:

on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-phyloseq >=1.54.0,<1.55.0
on bioconductor-sva >=3.58.0,<3.59.0
on r-base >=4.5,<4.6.0a0
on r-cluster
on r-dplyr
on r-ggplot2
on r-gridextra
on r-lme4
on r-lmertest
on r-magrittr
on r-matrix
on r-pheatmap
on r-rmarkdown
on r-ruv
on r-tibble
on r-tidyr
on r-vegan

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-mbecs

to add into an existing workspace instead, run:

pixi add bioconductor-mbecs

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-mbecs

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mbecs

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-mbecs:<tag>

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