Package Recipe 'bioconductor-metaboannotation'

recipe bioconductor-metaboannotation

Utilities for Annotation of Metabolomics Data

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

High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

package bioconductor-metaboannotation¶

Versions:

1.14.0-0, 1.10.0-0, 1.6.1-0, 1.4.1-0, 1.2.0-0

Depends:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-compounddb >=1.14.0,<1.15.0
on bioconductor-metabocoreutils >=1.18.0,<1.19.0
on bioconductor-mscoreutils >=1.22.0,<1.23.0
on bioconductor-protgenerics >=1.42.0,<1.43.0
on bioconductor-qfeatures >=1.20.0,<1.21.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-spectra >=1.20.0,<1.21.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0

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-metaboannotation

to add into an existing workspace instead, run:

pixi add bioconductor-metaboannotation

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-metaboannotation

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-metaboannotation

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-metaboannotation:<tag>

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