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MALDIrppa

MALDI mass spectrometry data robust pre-processing and other helper functions

https://github.com/japal/maldirppa

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary

Keywords

mass-spectrometry pre-processing r-package
Last synced: 6 months ago · JSON representation

Repository

MALDI mass spectrometry data robust pre-processing and other helper functions

Basic Info
  • Host: GitHub
  • Owner: Japal
  • Language: TeX
  • Default Branch: master
  • Homepage:
  • Size: 17.4 MB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Topics
mass-spectrometry pre-processing r-package
Created over 9 years ago · Last pushed 7 months ago
Metadata Files
Readme

README.md

MALDIrppa

MALDI mass spectrometry data robust pre-processing and other helper functions

R build status <!-- badges: end -->

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::installurl(url="https://github.com/Japal/MALDIrppa/archive/master.zip", INSTALLopt= "--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.

Owner

  • Name: Javier Palarea-Albaladejo
  • Login: Japal
  • Kind: user
  • Location: Girona, Spain
  • Company: University of Girona

GitHub Events

Total
  • Watch event: 1
  • Push event: 1
Last Year
  • Watch event: 1
  • Push event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 88
  • Total Committers: 3
  • Avg Commits per committer: 29.333
  • Development Distribution Score (DDS): 0.068
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Japal j****a@b****k 82
Sebastian Gibb m****l@s****e 4
Paolo Ribeca p****a@g****m 2
Committer Domains (Top 20 + Academic)
sebastiangibb.de: 1 bioss.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 18
  • Total pull requests: 3
  • Average time to close issues: 10 days
  • Average time to close pull requests: 5 days
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 1.5
  • Average comments per pull request: 1.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sgibb (16)
  • HBrendy (1)
  • Rutaiwan (1)
Pull Request Authors
  • sgibb (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 387 last-month
  • Total docker downloads: 21,154
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: MALDIrppa

MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis

  • Versions: 12
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 387 Last month
  • Docker Downloads: 21,154
Rankings
Docker downloads count: 12.6%
Forks count: 14.2%
Dependent packages count: 18.1%
Average: 22.5%
Dependent repos count: 23.9%
Stargazers count: 27.8%
Downloads: 38.0%
Maintainers (1)
javier.palarea@udg.edu
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • MALDIquant * depends
  • R >= 3.2.5 depends
  • lattice * depends
  • robustbase * depends
  • signal * depends
  • waveslim * depends
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests