Package Recipe 'bioconductor-squallms'

recipe bioconductor-squallms

Speedy quality assurance via lasso labeling for LC-MS data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/squallms.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-squallms/meta.yaml

squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.

package bioconductor-squallms¶

Versions:

1.4.0-0

Depends:

on bioconductor-msexperiment >=1.12.0,<1.13.0
on bioconductor-msnbase >=2.36.0,<2.37.0
on bioconductor-xcms >=4.8.0,<4.9.0
on r-base >=4.5,<4.6.0a0
on r-caret
on r-data.table
on r-dplyr
on r-ggplot2
on r-keys
on r-plotly
on r-rams
on r-shiny
on r-tibble
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-squallms

to add into an existing workspace instead, run:

pixi add bioconductor-squallms

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-squallms

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-squallms

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-squallms:<tag>

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