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gogogpcr

https://github.com/hausergroup/gogogpcr

Science Score: 65.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization hausergroup has institutional domain (drug.ku.dk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary

Keywords

python
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: HauserGroup
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 7.41 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Topics
python
Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

gogoGPCR

Note that this repo is deprecated. All code used for these analyses can now be found in a better documented and more accessible version in Hausergroup/gogoGPCR2. Please do not hesitate to contact the authors with inquiries regarding the analyses or code.

       

Code style: black

gogoGPCR is a framework for performing burden testing on UK Biobank Whole-Exome Sequencing (WES) data. This repo contains a series of notebooks for pre-processing and quality-controlling UKB VCF files, mainly with Hail, a Dockerfile for pre-processing phenotypes with PHESANT, and a series of Shell scripts for performing burden testing, with regenie.

Despite the name, gogoGPCR can, in principle, be run for any gene (or set hereof).

For information on running individual notebooks, see notebooks/README.md. Likewise, see scripts/README.md for running individual scripts.

WARNING: gogoGPCR will probably (99% confidence) not work out of the box and requires tweaking for your particular setup. In the very least, it may serve as inspiration for your own analyses.

Usage

Notebooks and scripts should generally be run in numerical order. Notebook/scripts starting with 0*_ e.g. notebooks/02_covariates.py, need only be run once and the generated file can be re-used for further analyses. Files wigth *a,b,c_ e.g. 03c_metabolic_phenotypes_BT.py represent different versions of the same step.

Structure

``` ├── README.md ├── config.toml # Majority of configuration ├── notebooks # Pre-processing and QC Jupyter notebooks │ ├── 00prescriptions.py
│ ├── 01samplehardfilter.py
│ ├── ... │ ├── 4forestplots.py │ └── README.md ├── docker # Dockerfile for running PHESANT │ └── phesant
│ ├── installpackages.R
│ └── Dockerfile ├── scripts # Shell scripts for running regenie step 1 and 2 │ ├── 00mergefiles.sh │ ├── ... │ ├── 1aregeniestep1BT.sh │ ├── 2aregeniestep2BT.sh │ └── README.md
├── src # QC and utility functions │ ├── matrixtables.py │ ├── ... │ └── utils.py
├── data │ ├── examples # Example regenie output │ │ └── *.regenie │ └── misc # Miscellaneous data files for mapping purposes │ ├── DataDictionaryCustom.csv │ ├── ... │ └── xgenplusspikein.b38.bed └───thesis # Please don't cite └── MScThesis.pdf

```

Prefer .ipynb notebooks?

Run jupytext --from py:percent --to notebook notebooks/*.py

Citation

van der Velden, W. J. C., Lindquist, P., Madsen, J. S., Stassen, R. H. M. J., Wewer Albrechtsen, N. J., Holst, J. J., Hauser, A. S., & Rosenkilde, M. M. (2021). Molecular and in vivo phenotyping of missense variants of the human glucagon receptor. Journal of Biological Chemistry, 0(0), 101413. https://doi.org/10.1016/j.jbc.2021.101413

Owner

  • Name: Hauser group
  • Login: HauserGroup
  • Kind: organization
  • Location: Denmark

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Sture Madsen"
    given-names: "Mona"
    orcid: "https://orcid.org/0000-0002-2841-7284"
  - family-names: "Hauser"
    given-names: "Alexander"
    orcid: "https://orcid.org/0000-0003-1098-6419"
title: "gogoGPCR"
version: 0.1.0
date-released: 2021-11-18
url: "https://github.com/jsture/gogoGPCR"
preferred-citation:
  type: article
  authors:
    - family-names: "van der Velden"
      given-names: "Wijnand J C"
    - family-names: "Lindquist"
      given-names: "Peter"
    - family-names: "Sture Madsen"
      given-names: "Mona"
      orcid: "https://orcid.org/0000-0002-2841-7284"
    - family-names: "Hauser"
      given-names: "Alexander"
      orcid: "https://orcid.org/0000-0003-1098-6419"
  doi: "10.1016/j.jbc.2021.101413"
  url: "ttps://www.sciencedirect.com/science/article/pii/S0021925821012229"
  journal: "Journal of Biological Chemistry"
  month: 11
  title: "Molecular and in vivo phenotyping of missense variants of the human glucagon receptor"
  year: 2021

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