https://rformassspectrometry.github.io/MsCoreUtils/

Core Utils for Mass Spectrometry Data
https://rformassspectrometry.github.io/MsCoreUtils/

bioconductor mass-spectrometry metabolomics proteomics rstats utils

Last synced: 3 months ago
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Core Utils for Mass Spectrometry Data

• Host: GitHub
• URL: https://rformassspectrometry.github.io/MsCoreUtils/
• Owner: rformassspectrometry
• Created: 2019-07-16T13:41:22.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2024-04-22T09:38:15.000Z (7 months ago)
• Last Synced: 2024-07-19T04:17:20.412Z (4 months ago)
• Topics: bioconductor, mass-spectrometry, metabolomics, proteomics, rstats, utils
• Language: R
• Homepage: https://rformassspectrometry.github.io/MsCoreUtils/
• Size: 12.5 MB
• Stars: 16
• Watchers: 6
• Forks: 11
• Open Issues: 10
• Metadata Files:
  • Readme: README.md

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README

        
# Low level functions for MS data

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

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

[![codecov](https://codecov.io/gh/rformassspectrometry/MsCoreUtils/branch/main/graph/badge.svg?token=sv2V5zQjib)](https://codecov.io/gh/rformassspectrometry/MsCoreUtils)

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

[![years in bioc](http://bioconductor.org/shields/years-in-bioc/MsCoreUtils.svg)](https://bioconductor.org/packages/release/bioc/html/MsCoreUtils.html)

[![Ranking by downloads](http://bioconductor.org/shields/downloads/release/MsCoreUtils.svg)](https://bioconductor.org/packages/stats/bioc/MsCoreUtils/)

[![build release](http://bioconductor.org/shields/build/release/bioc/MsCoreUtils.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/MsCoreUtils/)

[![build devel](http://bioconductor.org/shields/build/devel/bioc/MsCoreUtils.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/MsCoreUtils/)

`MsCoreUtils` defines low-level functions for mass spectrometry data

and is independent of any high-level data structures.  These functions

include mass spectra processing functions (noise estimation,

smoothing, binning, baseline estimation), quantitative aggregation

functions (median polish, robust summarisation, ...), missing data

imputation, data normalisation (quantiles, vsn, ...)  as well as misc

helper functions, that are used across high-level data structure

within the [R for Mass Spectrometry

packages](https://www.rformassspectrometry.org/pkgs/).

See the package [homepage](https://rformassspectrometry.github.io/MsCoreUtils)

for more information.

# Installation

The package can be installed with

```r

install.packages("BiocManager")

BiocManager::install("MsCoreUtils")

```

# 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).

## Previous external contributions

- Sigurdur Smarason (@SiggiSmara): weighted moving average (https://github.com/sgibb/MALDIquant/pull/54)

- Thomas Naake (@tnaake): dotproduct calculation (https://github.com/rformassspectrometry/MsCoreUtils/pull/17)

- Adriaan Sticker: `robustSummary` aggregation function (originally contributed to `MSnbase`)