Variant Effect Prediction Python Packages

caddsv

CADD-SV – a framework to score the effect of structural variants

mmsplice

Tissue-specific variant effect predictions on splicing

deepvregulome

DeepVRegulome is an end‑to‑end framework for predicting the functional impact of small somatic variants in non‑coding regulatory regions (splice sites and transcription‑factor‑binding sites) using fine‑tuned DNABERT models.

gpn

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

spliceai-pytorch

Implementation of SpliceAI, Illumina's deep neural network to predict variant effects on splicing, in PyTorch.

eve-pytorch

Implementation of evolutionary model of variant effect (EVE), a deep generative model of evolutionary data, in PyTorch.

sequence-unet

Fully convolutional deep learning variant effect predictor architecture