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Hoeze committed Feb 26, 2025
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# AbExp variant effect prediction pipeline

AbExp is a tool to predict aberrant gene underexpression in 48 human tissue based on DNA sequence variants.
AbExp is a tool to predict aberrant gene expression in 49 human tissue based on DNA sequence variants.
It was trained on aberrant gene expression calls from the GTEx dataset.

This repository contains a bioinformatics software pipeline for calculating **AbExp variant effect predictions**, taking vcf files as input.
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## Setup

1) install conda and mamba on your system
1) install conda and mamba on your system.

Tip: Use the [conda-libmamba-solver](https://conda.github.io/conda-libmamba-solver/user-guide/) for an improved experience when installing environments with `conda`!
2) To download the VEP cache (if not existing yet):
```bash
VEP_CACHE_PATH="<your cache path here>"
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