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https://github.com/rformassspectrometry/msio

Serializing/importing mass spectrometry data objects eventually using language-agnostic formats.
https://github.com/rformassspectrometry/msio

mass-spectrometry metabolomics proteomics

Last synced: about 1 month ago
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Serializing/importing mass spectrometry data objects eventually using language-agnostic formats.

Host: GitHub
URL: https://github.com/rformassspectrometry/msio
Owner: rformassspectrometry
Created: 2024-06-12T07:06:36.000Z (6 months ago)
Default Branch: main
Last Pushed: 2024-10-25T09:18:38.000Z (about 2 months ago)
Last Synced: 2024-10-25T14:32:51.124Z (about 2 months ago)
Topics: mass-spectrometry, metabolomics, proteomics
Language: R
Homepage: https://rformassspectrometry.github.io/MsIO
Size: 3.82 MB
Stars: 2
Watchers: 3
Forks: 0
Open Issues: 2
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md

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README

        # MsIO

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

[![R-CMD-check-bioc](https://github.com/RforMassSpectrometry/MsIO/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/RforMassSpectrometry/MsIO/actions?query=workflow%3AR-CMD-check-bioc)

[![codecov](https://codecov.io/gh/rformassspectrometry/MsIO/graph/badge.svg?token=M4yYzef5mK)](https://codecov.io/gh/rformassspectrometry/MsIO)

[![:name status badge](https://rformassspectrometry.r-universe.dev/badges/:name)](https://rformassspectrometry.r-universe.dev/)

[![license](https://img.shields.io/badge/license-Artistic--2.0-brightgreen.svg)](https://opensource.org/licenses/Artistic-2.0)

The *MsIO* package supports serializing and restoring/importing mass

spectrometry (MS) data objects to and from language agnostic file

formats. Ultimately, this package aims at enabling an easier exchange of data

and results between different software tools and programming languages.

R provides with the `save()` and `load()` functions a possibility to serialize

(and later import) variables and objects to disk, but the data is stored in a

R-specific binary format which is not easily readable by other programming

languages or software tools. Exchange of data and results between programming

languages and tools is however important to avoid the need to re-implement

methodology and algorithms and make the most of existing software to create

powerful analysis workflow.

The *MsIO* package defines generic export/import methods along with *parameter*

objects that allow to select and configure the file format(s). Where possible,

it is integrated with other approaches in

[Bioconductor](https://bioconductor.org) such as the

[*alabaster.base*](https://doi.org/doi:10.18129/B9.bioc.alabaster.base)

package. In particular *MsIO* will integrate with *alabaster.base* providing

`saveObject()` methods for exporting/importing MS specific data objects to JSON

file formats, but, on top of that, supporting serializing MS data objects in

additional different formats and thus supporting specific file formats defined

by other software.

## Currently supported and implemented storage representations

The currently available export/data storage formats along with the respective

*parameter* object to configure the export/import are listed below:

- `PlainTextParam`: Export to or import from plain text files. For most

  objects the data is stored in simple tabulator delimited text files.

  Export/import can be configured with the `PlainTextParam` *parameter* class

  and is supported at present for `MsBackendMzR` and `Spectra` objects from the

  [*Spectra*](https://github.com/RforMassSpectrometry/Spectra) package,

  `MsExperiment` objects from the

  [*MsExperiment*](https://github.com/RforMassSpectrometry/MsExperiment) package

  and `XcmsExperiment` objects from the

  [*xcms*](https://github.com/sneumann/xcms) package.

- `AlabasterParam`: Export or import based on *alabaster*. The alabaster format

  stores the data in a structured way using standard file formats including

  HDF5 and JSON ensuring thus across programming language compatibility.

- `mzTabParam`: [*xcms*](https://github.com/sneumann/xcms) preprocessing

  results (i.e., from `XcmsExperiment` objects) can be exported in [mzTab-M

  format](https://hupo-psi.github.io/mzTab/).

- `MetaboLightsParam`: Import MS data experiments (including MS data files)

  from the public [MetaboLights](https://www.ebi.ac.uk/metabolights/)

  repository.

# Contributions

Contributions are highly welcome and should follow the [contribution

guidelines](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions).

Also, please check the coding style guidelines in the [RforMassSpectrometry

vignette](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html).

# License

The *MsIO* code is provided under a permissive [Artistic 2.0

license](https://opensource.org/licenses/Artistic-2.0). The

documentation, including the manual pages and the vignettes, are

distributed under a [CC BY-SA

license](https://creativecommons.org/licenses/by-sa/4.0/).