Package Recipe 't1dgrs2'

recipe t1dgrs2

Generate a Type 1 Diabetes Genetic Risk Score (T1D GRS) that accounts for interactions between HLA DR-DQ risk haplotypes.

Homepage:: https://github.com/t2diabetesgenes/t1dgrs2
License:: GPL / GPLv3
Recipe:: /t1dgrs2/meta.yaml

An improved T1D GRS (by Sharp et al., 2019) that incorporates both non-HLA and HLA risk components in discriminating between cases and controls, by accounting for interactions between HLA DR-DQ haplotype combinations. This uses 67 T1D-associated variants in either GRCh37 or GRCh38 to perform both a linear scoring of the genetic risk, with the added HLA DR-DQ interaction effect for the final GRS.

This Python package can be used on both imputed genotyping array and next generation sequencing (e.g., whole genome sequencing) input datasets, but will require quality control procedures to be applied beforehand.

Required: PLINK 1.9 fileset (.bed, .bim, .fam).

Please download all configuration files under the 'data' directory from the [Github page](https://github.com/t2diabetesgenes/t1dgrs2) and adjust paths in 't1dgrs2_setttings.yml' accordingly.

### Authors * Diane P Fraser ([email](mailto:d.p.fraser@exeter.ac.uk)) * Seth A Sharp ([email](mailto:ssharp@stanford.edu)) * Ankit M Arni ([email](mailto:a.m.arni@exeter.ac.uk)) * Richard A Oram ([email](mailto:r.oram@exeter.ac.uk)) * Michael N Weedon ([email](mailto:m.n.weedon@exeter.ac.uk)) * Kashyap A Patel ([email](mailto:k.a.patel@exeter.ac.uk))

### References 1. Oram RA, Patel K, Hill A, et al. (2016) A Type 1 Diabetes Genetic Risk Score Can Aid Discrimination Between Type 1 and Type 2 Diabetes in Young Adults. Diabetes Care 39(3): 337-344. [10.2337/dc15-1111](https://doi.org/10.2337/dc15-1111). 2. Patel KA, Oram RA, Flanagan SE, et al. (2016) Type 1 Diabetes Genetic Risk Score: A Novel Tool to Discriminate Monogenic and Type 1 Diabetes. Diabetes 65(7): 2094-2099. [10.2337/db15-1690](https://doi.org/10.2337/db15-1690). 3. Sharp SA, Rich SS, Wood AR, et al. (2019) Development and Standardization of an Improved Type 1 Diabetes Genetic Risk Score for Use in Newborn Screening and Incident Diagnosis. Diabetes Care 42(2): 200-207. [10.2337/dc18-1785](https://doi.org/10.2337/dc18-1785).

package t1dgrs2¶

Versions:

0.1.2-0, 0.1.1-0, 0.1.0-0

Depends:

on numpy 1.24.*
on pandas 1.5.*
on plink
on python >=3.11
on pyyaml 6.0.*
on scipy 1.10.*
on setuptools 67.6.*
on wheel 0.40.*

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install t1dgrs2

to add into an existing workspace instead, run:

pixi add t1dgrs2

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install t1dgrs2

Alternatively, to install into a new environment, run:

conda create -n envname t1dgrs2

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/t1dgrs2:<tag>

(see t1dgrs2/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/t1dgrs2/README.html)