- recipe bioconductor-mqmetrics
Quality Control of Protemics Data
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/MQmetrics.html
- License:
GPL-3
- Recipe:
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:
on r-base
>=4.3,<4.4.0a0on r-cowplot
on r-dplyr
on r-ggforce
on r-gghalves
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-gridextra
on r-gtable
on r-knitr
on r-magrittr
on r-plyr
on r-purrr
on r-rcolorbrewer
on r-readr
on r-reshape2
on r-rlang
on r-rmarkdown
on r-scales
on r-stringr
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-mqmetrics
to add into an existing workspace instead, run:
pixi add bioconductor-mqmetrics
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-mqmetrics
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-mqmetrics
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-mqmetrics:<tag>
(see bioconductor-mqmetrics/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:
[](http://bioconda.github.io/recipes/bioconductor-mqmetrics/README.html)
