variant-effect-prediction

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

One interface to nine genomic deep-learning oracles — variant effect prediction, calibrated per-track percentiles, and plain-English analysis through MCP.

Tissue-specific variant effect predictions on splicing

Clinical Whole Genome and Exome Sequencing Pipeline

MarinDNA - open development of genomic language models

Fully convolutional deep learning variant effect predictor architecture

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

Predicting the effect of mutations on protein stability and protein binding affinity using pretrained neural networks and a ranking objective function.

We present Envision, an accurate predictor of protein variant molecular effect, trained using large-scale experimental mutagenesis data. All data and software in this study are freely available. The training data set and all code used to train the models and generate the figures presented in this manuscript are available here. Envision predictio…

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

Pipeline for variant annotation using Variant Effect Predictor (VEP)

Collection of variant effect prediction models, webapp to list them as well as DVC pipeline to do benchmarking experiments against proteingym-base datasets.

Infrastructure for facilitating variant effect prediction using machine learning. Data class to combine assay, sequence, MSA and structure data to a coherent data package. Model cards for supervised and zeroshot ML models.

Workflow to Explore and Analyze Variants of Eukaryotic Populations

Integrative framework combining TF footprinting with genome-wide association analyses to identify causal noncoding variants and elucidate their regulatory mechanisms in gene regulation

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.

VEP-bench

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

NCypher — honest, context-specific triage of non-coding regulatory variants in paediatric DMG. Built with Claude: Life Sciences (Researcher track).