recipe bioconductor-ipo

Automated Optimization of XCMS Data Processing parameters

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/IPO.html

License:

GPL (>= 2) + file LICENSE

Recipe:

/bioconductor-ipo/meta.yaml

Links:

biotools: ipo

The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.

package bioconductor-ipo

(downloads) docker_bioconductor-ipo

Versions:
1.36.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0, 

1.36.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.1-1,  1.8.1-0,  1.4.0-0,  1.2.2-0,  1.0.0-0

Depends:

  • on bioconductor-biocparallel >=1.44.0,<1.45.0

  • on bioconductor-camera >=1.66.0,<1.67.0

  • on bioconductor-xcms >=4.8.0,<4.9.0

  • on r-base >=4.5,<4.6.0a0

  • on r-rsm

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-ipo

to add into an existing workspace instead, run:

pixi add bioconductor-ipo

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-ipo

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ipo

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-ipo:<tag>

(see bioconductor-ipo/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.

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