Package Recipe 'bioconductor-cosmiq'

recipe bioconductor-cosmiq

cosmiq - COmbining Single Masses Into Quantities

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/cosmiq.html
License:: GPL-3
Recipe:: /bioconductor-cosmiq/meta.yaml
Links:: biotools: cosmiq, doi: 10.5167/uzh-107947

cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.

package bioconductor-cosmiq¶

Versions:

1.44.0-0, 1.40.0-0, 1.36.0-0, 1.34.0-0, 1.32.0-1, 1.32.0-0, 1.28.0-2, 1.28.0-1, 1.28.0-0,

1.44.0-0, 1.40.0-0, 1.36.0-0, 1.34.0-0, 1.32.0-1, 1.32.0-0, 1.28.0-2, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.22.0-0, 1.20.0-1, 1.18.0-1, 1.16.1-0, 1.16.0-0, 1.12.0-0

Depends:

on bioconductor-faahko >=1.50.0,<1.51.0
on bioconductor-faahko >=1.50.0,<1.51.0a0
on bioconductor-massspecwavelet >=1.76.0,<1.77.0
on bioconductor-massspecwavelet >=1.76.0,<1.77.0a0
on bioconductor-xcms >=4.8.0,<4.9.0
on bioconductor-xcms >=4.8.0,<4.9.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-pracma
on r-rcpp

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-cosmiq

to add into an existing workspace instead, run:

pixi add bioconductor-cosmiq

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-cosmiq

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cosmiq

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-cosmiq:<tag>

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