Topic: "variant-effect-prediction"
songlab-cal/gpn
Genomic Pre-trained Network
Language: Jupyter Notebook - Size: 52.1 MB - Last synced at: 21 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: 5 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: 19 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

FowlerLab/Envision2017
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: 20 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: 7 days ago - Pushed at: 7 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: 15 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: 15 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

IBCHgenomic/varlinker
variant linker for genome annotation
Language: Rust - Size: 0 Bytes - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

IBCHgenomic/genovaranno
Variant annotation human genomics
Language: Rust - Size: 344 KB - Last synced at: 7 days ago - Pushed at: 8 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: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

kkwock/VARify
Transcriptional variant verification to validate predicted variants from genomic data in expressed transcripts
Language: HTML - Size: 48.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

jhrcook/protein-language-models
Experimenting with protein language model predictions
Language: Python - Size: 3.91 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

anilprakash94/neur_ally
Deep learning model for non-coding regulatory variants
Language: Python - Size: 4.85 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

kopalgarg/variantviewer
interactive variant tables for easy filtering
Language: R - Size: 2 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
