recipe bioconductor-lipidr

Data Mining and Analysis of Lipidomics Datasets

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-lipidr/meta.yaml

lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.

package bioconductor-lipidr

versions:

2.20.0-0,  2.16.0-0,  2.14.1-0,  2.12.0-0,  2.8.0-0,  2.6.0-0,  2.4.0-1,  2.4.0-0,  2.2.0-0, 

2.20.0-0,  2.16.0-0,  2.14.1-0,  2.12.0-0,  2.8.0-0,  2.6.0-0,  2.4.0-1,  2.4.0-0,  2.2.0-0,  2.0.0-0,  1.0.0-1

depends bioconductor-fgsea:

>=1.32.0,<1.33.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-ropls:

>=1.38.0,<1.39.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-dplyr:

depends r-forcats:

depends r-ggplot2:

depends r-imputelcmd:

depends r-magrittr:

depends r-rlang:

depends r-tidyr:

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-lipidr

and update with::

   mamba update bioconductor-lipidr

To create a new environment, run:

mamba create --name myenvname bioconductor-lipidr

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-lipidr:<tag>

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

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