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targene-pipeline

Nextflow pipeline for Targeted-Learning of genetic effects

https://github.com/targene/targene-pipeline

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
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    .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (9.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Nextflow pipeline for Targeted-Learning of genetic effects

Basic Info
  • Host: GitHub
  • Owner: TARGENE
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Homepage:
  • Size: 11.2 MB
Statistics
  • Stars: 11
  • Watchers: 3
  • Forks: 0
  • Open Issues: 7
  • Releases: 34
Created over 4 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

TarGene-Pipeline

TarGene is a Nextflow pipeline for the estimation of genetic effects on human traits using highly flexible semi-parametric inference methods (Targeted Minimum Loss-Based Estimation, One-Step Estimation).

Is TarGene for you?

If you would like to use flexible machine-learning methods while preserving valid statistical inference and your project falls within any of the following, then the answer is Yes!

Supported study designs:

  • GWAS
  • PheWAS
  • Custom

Supported databases:

  • UK Biobank
  • All of Us
  • Custom

Supported genetic effects: - Main effects - Interactions up to any order

Documentation Access

Want to know more? Please visit the docs.

Running the Workflow

TarGene is a Nextflow pipeline, please refer to their documentation for general usage. The main point being that, depending on your HPC specifications, you will need to provide a specific myplatform.config configuration file on top of your project myproject.config configuration file.

bash nextflow run TARGENE/targene-pipeline -c myplatform.config -c myproject.config -resume

Owner

  • Name: TarGene
  • Login: TARGENE
  • Kind: organization

Targeted Estimation of Genetic Effects

JOSS Publication

TarGene: A Nextflow pipeline for the estimation of genetic effects on human traits via semi-parametric methods.
Published
March 24, 2026
DOI
Volume 11, Issue 119, Page 9603
Authors
Olivier Labayle ORCID
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom., School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
Joshua Slaughter ORCID
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom., School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
Breeshey Roskams-Hieter ORCID
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom., School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
Kelsey Tetley-Campbell
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom., School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
Mark J. van der Laan ORCID
Division of Biostatistics, University of California, Berkeley, CA, United States of America
Chris P. Ponting ORCID
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
Ava Khamseh ORCID
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom., School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom, Division of Biostatistics, University of California, Berkeley, CA, United States of America
Sjoerd Viktor Beentjes ORCID
MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom., School of Mathematics and Maxwell Institute for Mathematical Sciences, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom, Division of Biostatistics, University of California, Berkeley, CA, United States of America
Editor
Abhishek Tiwari ORCID
Tags
nextflow statistics semi-parametric statistics population genetics genetic effects causal inference
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Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Labayle"
  given-names: "Olivier"
- family-names: "Tetley-Campbell"
  given-names: "Kelsey"
- family-names: "Slaughter"
  given-names: "Joshua"
- family-names: "Roskams-Hieter"
  given-names: "Breeshey"
- family-names: "Beentjes"
  given-names: "Sjoerd"
- family-names: "Khamseh"
  given-names: "Ava"
- family-names: "Ponting"
  given-names: "Chris"
title: "TarGene"
url: "https://github.com/TARGENE/targene-pipeline"

GitHub Events

Total
  • Create event: 9
  • Release event: 1
  • Issues event: 9
  • Delete event: 6
  • Issue comment event: 10
  • Push event: 99
  • Pull request review comment event: 27
  • Pull request review event: 28
  • Pull request event: 12
Last Year
  • Create event: 9
  • Release event: 1
  • Issues event: 9
  • Delete event: 6
  • Issue comment event: 10
  • Push event: 99
  • Pull request review comment event: 27
  • Pull request review event: 28
  • Pull request event: 12

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 107
  • Total pull requests: 31
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 0.37
  • Average comments per pull request: 0.48
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • olivierlabayle (138)
  • roskamsh (7)
  • jqian2015 (1)
  • k-tetley-campbell (1)
Pull Request Authors
  • olivierlabayle (27)
  • roskamsh (9)
  • github-actions[bot] (4)
  • k-tetley-campbell (3)
  • jeskowagner (1)
Top Labels
Issue Labels
enhancement (13) question (5)
Pull Request Labels
enhancement (2) bug (1)

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v2 composite
  • julia-actions/julia-buildpkg v1 composite
  • julia-actions/setup-julia v1 composite