Data for: \"Generative prediction of causal gene sets responsible for complex traits\"

The relationship between genotype and phenotype remains an outstanding question for organism-level traits because these traits are generally complex. The challenge arises from complex traits being determined by a combination of multiple genes (or loci), which leads to an explosion of possible genotype-phenotype mappings. The primary techniques to resolve these mappings are genome/transcriptome-wide association studies, which are limited by their lack of causal inference and statistical power.  Here, we develop an approach that leverages transcriptional data endowed with causal information and a generative machine learning model to strengthen statistical power.  Our implementation of the approach-- dubbed TWAVE---includes a variational autoencoder trained on human transcriptional data, which is incorporated into an optimization framework. TWAVE generates trait expression profiles, which we dimensionally reduce by identifying independently varying generalized pathways (eigengene..., Data were collected from GEO., , # Generative prediction of causal gene sets responsible for complex traits

[https://doi.org/10.5061/dryad.s4mw6m9hf](https://doi.org/10.5061/dryad.s4mw6m9hf)

## Description of the data and file structure

This is the data repository for the project 'Generative prediction of causal gene sets responsible for complex traits'.

This repository contains data to run Jupyter notebooks and a Python script in the associated Zenodo code repository (doi: 10.5281/zenodo.12955283).

Data: 1) single-cell RNAseq data on the human complex disease traits featured in the
manuscript (labeled by GEO series, see Table 1 in main text). In the files below, the traits are labeled by their abbreviations and GEO series:

* tep = Non-small cell lung cancer (GSE89843)
* t1d = Type-1 diabetes (GSE182870)
* MODY3 = Maturity-onset diabetes of the young type 3 (GSE129653)
* ib = Inflammatory bowel (GSE193677)
* cancermeta = Cancer metastasis (GSE202695)
* asthma = Allergic asthma (GSE96783)
* allergy = Food allergy ...,