variant-effect-prediction | Topic

Topic: "variant-effect-prediction"

songlab-cal/gpn

Genomic Pre-trained Network

Language: Jupyter Notebook - Size: 52.1 MB - Last synced at: 25 days ago - Pushed at: 3 months ago - Stars: 266 - Forks: 40

gagneurlab/MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing

Language: Jupyter Notebook - Size: 82.3 MB - Last synced at: 9 days ago - Pushed at: about 2 years ago - Stars: 42 - Forks: 21

allydunham/sequence_unet

Fully convolutional deep learning variant effect predictor architecture

Language: Python - Size: 2.12 MB - Last synced at: 23 days ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 4

OpenOmics/genome-seek

Clinical Whole Genome and Exome Sequencing Pipeline

Language: Python - Size: 849 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 18 - Forks: 11

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 predictions, along with feature annotations, are available at https://envision.gs.washington.edu/.

Language: Jupyter Notebook - Size: 6 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 16 - Forks: 1

kircherlab/CADD-SV

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

Language: Python - Size: 23.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 14 - Forks: 4

dohlee/spliceai-pytorch

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

Language: Jupyter Notebook - Size: 150 KB - Last synced at: 24 days ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 3

elaspic/elaspic2

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

Language: Jupyter Notebook - Size: 46.8 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 11 - Forks: 5

songlab-cal/TraitGym

Language: Jupyter Notebook - Size: 4.58 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 6 - Forks: 0

CERC-Genomic-Medicine/vep_pipeline

Pipeline for variant annotation using Variant Effect Predictor (VEP)

Language: Jupyter Notebook - Size: 581 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 4 - Forks: 1

dohlee/eve-pytorch

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

Language: Python - Size: 134 KB - Last synced at: 19 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

DeepRank/DeepRank-Mut 📦

Deep learning framework to predict functional effects of missense variants in human

Language: Python - Size: 187 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

allydunham/dms_mutations

Preliminary analysis of a combined DMS dataset, including clustering and VEP benchmark

Language: R - Size: 407 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

Matthew-Mosior/Basic-Variant-Parser

A Haskell script that performs basic parsing on the default output of ensembl-vep and variant-calling format (vcf) files.

Language: Haskell - Size: 4.96 MB - Last synced at: 19 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

IBCHgenomic/genovaranno

Variant annotation human genomics

Language: Rust - Size: 145 KB - Last synced at: about 16 hours ago - Pushed at: about 17 hours ago - Stars: 0 - Forks: 0

IBCHgenomic/varlinker

variant linker for genome annotation

Language: Rust - Size: 0 Bytes - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

Keonapang/RovHer

A heritability-optimized scoring method using multivariate adaptive regression splines that incorporates 75 variant- and gene-level features. RovHer leverages exome-wide association statistics to train models estimating the probability of RV functional impact.

Language: R - Size: 1.54 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

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