recipe bioconductor-mqmetrics

Quality Control of Protemics Data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-mqmetrics/meta.yaml

The package MQmetrics (MaxQuant metrics) provides a workflow to analyze the quality and reproducibility of your proteomics mass spectrometry analysis from MaxQuant.Input data are extracted from several MaxQuant output tables and produces a pdf report. It includes several visualization tools to check numerous parameters regarding the quality of the runs. It also includes two functions to visualize the iRT peptides from Biognosys in case they were spiked in the samples.

package bioconductor-mqmetrics

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-cowplot:

depends r-dplyr:

depends r-ggforce:

depends r-gghalves:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-gridextra:

depends r-gtable:

depends r-knitr:

depends r-magrittr:

depends r-plyr:

depends r-purrr:

depends r-rcolorbrewer:

depends r-readr:

depends r-reshape2:

depends r-rlang:

depends r-rmarkdown:

depends r-scales:

depends r-stringr:

depends r-tidyr:

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-mqmetrics

and update with::

   mamba update bioconductor-mqmetrics

To create a new environment, run:

mamba create --name myenvname bioconductor-mqmetrics

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-mqmetrics:<tag>

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

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