Package Recipe 'bioconductor-mspurity'

recipe bioconductor-mspurity

Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/msPurity.html
License:: GPL-3 + file LICENSE
Recipe:: /bioconductor-mspurity/meta.yaml
Links:: biotools: mspurity, doi: 10.1021/acs.analchem.6b04358

msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.

package bioconductor-mspurity¶

Versions:

1.36.0-0, 1.32.0-2, 1.32.0-1, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.0-2,

1.36.0-0, 1.32.0-2, 1.32.0-1, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.0-2, 1.20.0-1, 1.20.0-0, 1.18.0-0, 1.16.2-1, 1.16.2-0, 1.16.0-0, 1.14.0-0, 1.12.2-0, 1.12.1-0, 1.12.0-0, 1.10.0-1, 1.8.1-0, 1.8.0-0, 1.5.4-1, 1.5.4-0, 1.4.0-1, 1.4.0-0, 1.3.9-0

Depends:

on bioconductor-mzr >=2.44.0,<2.45.0
on bioconductor-mzr >=2.44.0,<2.45.0a0
on libblas >=3.9.0,<4.0a0
on libcxx >=19
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-dbi
on r-dbplyr
on r-dosnow
on r-dplyr
on r-fastcluster
on r-foreach
on r-ggplot2
on r-magrittr
on r-plyr
on r-rcpp
on r-reshape2
on r-rsqlite
on r-stringr

Additional platforms:

linux-aarch64, osx-arm64

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-mspurity

to add into an existing workspace instead, run:

pixi add bioconductor-mspurity

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-mspurity

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mspurity

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-mspurity:<tag>

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