recipe bioconductor-msquality

MsQuality - Quality metric calculation from Spectra and MsExperiment objects

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-msquality/meta.yaml

The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

package bioconductor-msquality

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-msdata:

>=0.42.0,<0.43.0

depends bioconductor-msexperiment:

>=1.4.0,<1.5.0

depends bioconductor-protgenerics:

>=1.34.0,<1.35.0

depends bioconductor-spectra:

>=1.12.0,<1.13.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

>=3.3.5

depends r-htmlwidgets:

>=1.5.3

depends r-plotly:

>=4.9.4.1

depends r-rmzqc:

>=0.5.0

depends r-shiny:

>=1.6.0

depends r-shinydashboard:

>=0.7.1

depends r-stringr:

>=1.4.0

depends r-tibble:

>=3.1.4

depends r-tidyr:

>=1.1.3

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-msquality

and update with::

   mamba update bioconductor-msquality

To create a new environment, run:

mamba create --name myenvname bioconductor-msquality

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-msquality:<tag>

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

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