Cite this dataset as
Pui, C.S., Fumagalli, M., Mathieson, S. (2023). Python code for building and training a generative adversarial network for demographic inferences from genomic data. NERC EDS Environmental Information Data Centre. (Model). https://doi.org/10.5285/3ae572f6-4862-47ae-b4a0-4b9c496b5b54
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This model code will be available under the terms of the Open Government Licence 
Python code for building and training a generative adversarial network for demographic inferences from genomic data
DISCLAIMER: Publication of this model code by the EIDC does not signify any endorsement or approval. By accessing and using the resource, you acknowledge that it is entirely at your own risk and you are solely responsible for any loss or liability that may arise.
A collection of python and bash scripts to implement, train and deploy a generative adversarial network for population genetic inferences.
The networks have been tuned to be deployed to genomic data from Anopheles mosquitoes. However, the general framework can be applied to other species.
It requires the input data to be in Variant Call Format (VCF) format and the simulations need to be in msprime format.
The networks have been tuned to be deployed to genomic data from Anopheles mosquitoes. However, the general framework can be applied to other species.
It requires the input data to be in Variant Call Format (VCF) format and the simulations need to be in msprime format.
Publication date: 2023-12-08
View record as
Formats
Python scripts
Bash scripts
R script
Provenance & quality
The methodology can be applied to up to two populations at the same time. The code uses the keras python package and the scripts have been tested via simulations. Inferences were tested using simulations with known output, and the power to infer the ground truth was recovered. Simulations can be performed using msprime or SLiM.
Correspondence/contact details
Authors
https://orcid.org/0009-0008-4956-1358 Other contacts
- Rights holder
-
Queen Mary University of London
- Custodian
-
NERC EDS Environmental Information Data Centreinfo@eidc.ac.uk
- Publisher
-
NERC EDS Environmental Information Data Centreinfo@eidc.ac.uk
Additional metadata
- Topic categories
- environment
- Keywords
- demographic inference , generative adversarial network , population genetics
- Funding
- Natural Environment Research Council Award: NE/X009637/1
- Last updated
- 08 February 2024 17:25