recipe bioconductor-plsdabatch

PLSDA-batch

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/PLSDAbatch.html

License:

GPL-3

Recipe:

/bioconductor-plsdabatch/meta.yaml

A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings.

package bioconductor-plsdabatch

versions:

1.2.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocstyle:

>=2.34.0,<2.35.0

depends bioconductor-mixomics:

>=6.30.0,<6.31.0

depends bioconductor-treesummarizedexperiment:

>=2.14.0,<2.15.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-ggpubr:

depends r-gridextra:

depends r-lmertest:

depends r-performance:

depends r-pheatmap:

depends r-rdpack:

depends r-scales:

depends r-vegan:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-plsdabatch

and update with::

   mamba update bioconductor-plsdabatch

To create a new environment, run:

mamba create --name myenvname bioconductor-plsdabatch

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-plsdabatch:<tag>

(see `bioconductor-plsdabatch/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an badge with the following MarkDown:

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