recipe bioconductor-mwastools

MWASTools: an integrated pipeline to perform metabolome-wide association studies

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MWASTools.html

License:

CC BY-NC-ND 4.0

Recipe:

/bioconductor-mwastools/meta.yaml

MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.

package bioconductor-mwastools

versions:

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0, 

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-kegggraph:

>=1.62.0,<1.63.0

depends bioconductor-keggrest:

>=1.42.0,<1.43.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-boot:

depends r-car:

depends r-ggplot2:

depends r-glm2:

depends r-gridextra:

depends r-igraph:

depends r-ppcor:

depends r-rcurl:

requirements:

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-mwastools

and update with::

   mamba update bioconductor-mwastools

To create a new environment, run:

mamba create --name myenvname bioconductor-mwastools

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-mwastools:<tag>

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

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