Package Recipe 'r-erah'

recipe r-erah

Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics.

Homepage:: https://CRAN.R-project.org/package=erah
License:: GPL-2.0-or-later
Recipe:: /r-erah/meta.yaml

Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.

package r-erah¶

Versions:

2.2.0-0, 2.0.1-1, 2.0.1-0, 2.0.0-0, 1.1.2-0

Depends:

on libgcc >=13
on libstdcxx >=13
on r-base >=4.4,<4.5.0a0
on r-furrr
on r-future
on r-hiclimr
on r-igraph
on r-osd
on r-progress
on r-quantreg
on r-signal
on r-tibble

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 r-erah

to add into an existing workspace instead, run:

pixi add r-erah

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 r-erah

Alternatively, to install into a new environment, run:

conda create -n envname r-erah

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/r-erah:<tag>

(see r-erah/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¶

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