ouks

🔴OUKS🔵 Omics Untargeted Key Script

https://github.com/plyush1993/ouks

Science Score: 67.0%

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Keywords

metabolomics r

Last synced: 10 months ago · JSON representation ·

Repository

🔴OUKS🔵 Omics Untargeted Key Script

Basic Info

Host: GitHub
Owner: plyush1993
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://plyush1993.github.io/OUKS/
Size: 31.6 MB

Statistics

Stars: 8
Watchers: 1
Forks: 2
Open Issues: 0
Releases: 11

Topics

metabolomics r

Created over 5 years ago · Last pushed 11 months ago

Metadata Files

Readme Changelog License Citation Roadmap

Omics Untargeted Key Script (OUKS)

Brief Description :old_key:

R based open-source collection of scripts called :redcircle:OUKS:largeblue_circle: (Omics Untargeted Key Script) providing comprehensive nine step LC-MS untargeted metabolomic profiling data processing toolbox :toolbox:

See website :computer:

Table of contents :clipboard:

Click to expand

- Instruction and introduction into the :red_circle:*OUKS* toolbox:large_blue_circle: are provided by [`Basic tutorial`](https://github.com/plyush1993/OUKS/blob/main/Basic%20tutorial.pdf) file. [`Session info`](https://github.com/plyush1993/OUKS/blob/main/Session%20Info.txt) and [`Used packages`](https://github.com/plyush1993/OUKS/blob/main/Used%20packages.pdf) are listed in corresponding files. - [Scripts](https://github.com/plyush1993/OUKS/tree/main/Scripts%20(R)) with comments, notes and references are stored in Scripts folder at a previously defined order along with [code](https://github.com/plyush1993/OUKS/blob/main/Scripts%20(R)/Figures%20for%20OUKS.R) for plotting figures associated with [article](https://doi.org/10.1021/acs.jproteome.1c00392). - [MS2 spectra](https://github.com/plyush1993/OUKS/tree/main/MS2%20spectra%20(mzXML)) for selected potential biomarkers of bladder cancer are stored in mzXML format at corresponding folder. - [Datasets](https://github.com/plyush1993/OUKS/tree/main/Datasets%20(csv)) in .csv and [other files](https://github.com/plyush1993/OUKS/tree/main/Auxiliary%20files%20(RData)) (.RData, .R) are available for reproducibility from corresponding folders. Files descriptions are provived by [`Roadmap`](https://github.com/plyush1993/OUKS/blob/main/Roadmap.pdf) file. Raw data (.CDF format) are available from [Metabolomics Workbench Repository](https://www.metabolomicsworkbench.org/), study ID: [ST001682](http://doi.org/10.21228/M8ZT4C). [`Metadata`](https://github.com/plyush1993/OUKS/blob/main/Datasets%20(csv)/metadata.csv) table is also provided. - [Report](https://github.com/plyush1993/OUKS/tree/main/Report%20(Rmd)) in [`.Rmd`](https://github.com/plyush1993/OUKS/blob/main/Report%20(Rmd)/Report%20example%20OUKS.Rmd), [`.pdf`](https://github.com/plyush1993/OUKS/blob/main/Report%20(Rmd)/Report-example-OUKS.pdf) and [`.docx`](https://github.com/plyush1993/OUKS/blob/main/Report%20(Rmd)/Report-example-OUKS.docx) formats were provided as an example to reproduce the *OUKS* code script. - [`Changelog`](https://github.com/plyush1993/OUKS/blob/main/CHANGELOG.md) file is provided and is constantly updated. See also [releases](https://github.com/plyush1993/OUKS/releases) page. - [Required packages](https://github.com/plyush1993/OUKS/tree/main/Required%20packages%20(archive)) section is for storing packages archives with strong version dependency. - Discussions, suggestions and error reports are [welcome](https://github.com/plyush1993/OUKS/issues).

Script | Purpose ------------ | ------------- 1. Randomization.R | experimental design and sample randomization 2. Integration.R | peaks integration and time alignment 3. Imputation.R | missing value imputation (MVI) and artifacts removal 4. Correction.R | signal drift correction and batch effect removal 5. Annotation.R | feature annotation and tentative identification by database search 6. Filtering.R | peaks filtering for quality checking and accounting of technical variation 7. Normalization.R | data normalization and adjusting of biological variation 8. Grouping.R | peaks grouping and molecular features clustering 9. Statistics.R | statistical analysis and hypothesis testing

Requirements :building_construction:

The only requirements are to be familiar with the basic syntax of the R language, PC with Internet connection and Windows OS (desirable), RStudio and R (≥ 4.1.2).

Citation :link:

OUKS has been published in the Journal of Proteome Research. If you use this software to analyze your own data, please cite it as below, thanks:

Ivan V. Plyushchenko, Elizaveta S. Fedorova, Natalia V. Potoldykova, Konstantin A. Polyakovskiy, Alexander I. Glukhov, and Igor A. Rodin Journal of Proteome Research 2022 21 (3), 833-847. DOI: 10.1021/acs.jproteome.1c00392

OUKS builds on many open-source software tools and open data sources. Therefore, it is important to also cite their work when using these algorithms via OUKS: 1, 2.

Contact :memo:

Please send any comment, suggestion or question you may have to the author (👨‍🔬 Dr. Ivan Plyushchenko):

Owner

Name: Ivan Plyushchenko
Login: plyush1993
Kind: user

Repositories: 3
Profile: https://github.com/plyush1993

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Plyushchenko"
  given-names: "Ivan V."
  orcid: "https://orcid.org/0000-0003-3883-4695"
title: "Omics Untargeted Key Script (OUKS)"
date-released: 2021-04-29
url: "https://github.com/plyush1993/OUKS"
preferred-citation:
  type: article
  authors:
  - family-names: "Plyushchenko"
    given-names: "Ivan V."
    orcid: "https://orcid.org/0000-0003-3883-4695"
  - family-names: "Fedorova"
    given-names: "Elizaveta S."
    orcid: "https://orcid.org/0000-0002-5774-7901"
  - family-names: "Potoldykova"
    given-names: "Natalia V."
  - family-names: "Polyakovskiy"
    given-names: "Konstantin A."
  - family-names: "Glukhov"
    given-names: "Alexander I."
  - family-names: "Rodin"
    given-names: "Igor A."
  doi: "10.1021/acs.jproteome.1c00392"
  journal: "J. Proteome Res."
  month: 3
  start: 833 # First page number
  end: 847 # Last page number
  title: "Omics Untargeted Key Script: R-Based Software Toolbox for Untargeted Metabolomics with Bladder Cancer Biomarkers Discovery Case Study"
  issue: 3
  volume: 21
  year: 2022

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