https://github.com/japal/maldirppa
MALDI mass spectrometry data robust pre-processing and other helper functions
https://github.com/japal/maldirppa
mass-spectrometry pre-processing r-package
Last synced: 3 months ago
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MALDI mass spectrometry data robust pre-processing and other helper functions
- Host: GitHub
- URL: https://github.com/japal/maldirppa
- Owner: Japal
- Created: 2016-07-07T06:55:12.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2025-07-27T15:37:45.000Z (6 months ago)
- Last Synced: 2025-10-22T05:59:43.759Z (3 months ago)
- Topics: mass-spectrometry, pre-processing, r-package
- Language: TeX
- Homepage:
- Size: 17.4 MB
- Stars: 3
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
Awesome Lists containing this project
README
# MALDIrppa
MALDI mass spectrometry data robust pre-processing and other helper functions
[](https://github.com/Japal/MALDIrppa/actions)
This package helps to implement a robust approach to deal with mass spectrometry (MS) data. It is aimed at alleviating reproducibility issues and pernicious effects of deviating signals on both data pre-processing and downstream data analysis. Based on robust statistical methods, it facilitates the identification and filtering of low-quality mass spectra and atypical peak profiles as well as monitoring and data handling through pre-processing, which extends existing computational tools for MS data. `MALDIrppa` integrates with and extends existing R packages for MS proteomics data. Helper functions are included that allow to export data into formats used for downstream analyses.
### Installation
The latest version of the package is available on CRAN and can be installed from R using
```
install.packages("MALDIrppa")
```
Alternatively, it can be installed from Github through the `devtools` package:
```
# For non-windows users
devtools::install_github(repo = "Japal/MALDIrppa")
# For windows users
devtools::install_url(url="https://github.com/Japal/MALDIrppa/archive/master.zip", INSTALL_opt= "--no-multiarch")
```
For compatibility with previous pre-processing pipelines, a previous version of MALDIrppa can be installed from source files. For example, for v1.0.5-1:
```
install.packages("https://cran.r-project.org/src/contrib/Archive/MALDIrppa/MALDIrppa_1.0.5-1.tar.gz", repo=NULL, type="source")
```
### Getting started
```
# Loading the library
library("MALDIrppa")
```
Documentation and examples are available through the help pages (`?MALDIrppa`).
### Illustrative pipeline
The package's vignette provides a walk through the main features and functions:
* Article on website: https://japal.github.io/MALDIrppa/
* CRAN: https://cran.r-project.org/web/packages/MALDIrppa/vignettes/MALDIrppa_vignette.html
### Citation
Palarea-Albaladejo J., McLean K., Wright F. and Smith (2018). MALDIrppa: quality control and robust analysis for mass spectrometry data. Bioinformatics 34(3):522–523.