Package Recipe 'bioconductor-metabcombiner'

recipe bioconductor-metabcombiner

Method for Combining LC-MS Metabolomics Feature Measurements

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/metabCombiner.html
License:: GPL-3
Recipe:: /bioconductor-metabcombiner/meta.yaml

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

package bioconductor-metabcombiner¶

Versions:

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.4.0-2, 1.4.0-1, 1.4.0-0,

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.4.0-2, 1.4.0-1, 1.4.0-0, 1.2.0-0, 1.0.1-0, 1.0.0-1

Depends:

on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-caret
on r-dplyr >=1.0
on r-matrixstats
on r-mgcv
on r-rlang
on r-tidyr

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-metabcombiner

to add into an existing workspace instead, run:

pixi add bioconductor-metabcombiner

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-metabcombiner

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-metabcombiner

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-metabcombiner:<tag>

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