variant-effect-prediction

There are 19 repositories under variant-effect-prediction topic.

  • songlab-cal/gpn

    Genomic Pre-trained Network

    Language:Jupyter Notebook19672724

  • gagneurlab/MMSplice_MTSplice

    Tissue-specific variant effect predictions on splicing

    Language:Jupyter Notebook4084521

  • allydunham/sequence_unet

    Fully convolutional deep learning variant effect predictor architecture

    Language:Python23354

  • 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 Notebook19326

  • OpenOmics/genome-seek

    Clinical Whole Genome and Exome Sequencing Pipeline

    Language:Python1812011

  • 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 Notebook17501

  • kircherlab/CADD-SV

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

    Language:Python144193

  • dohlee/spliceai-pytorch

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

    Language:Jupyter Notebook12313

  • CERC-Genomic-Medicine/vep_pipeline

    Pipeline for variant annotation using Variant Effect Predictor (VEP)

    Language:Jupyter Notebook5402

  • allydunham/dms_mutations

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

    Language:R1100

  • anilprakash94/neur_ally

    Deep learning model for non-coding regulatory variants

    Language:Python1100

  • DeepRank/DeepRank-Mut

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

    Language:Python1860

  • dohlee/eve-pytorch

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

    Language:Python120

  • 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:Haskell1100

  • AbhimanyuMandal/Germline-mutation

    Master's Thesis Project

    Language:Shell0100

  • kkwock/VARify

    Transcriptional variant verification to validate predicted variants from genomic data in expressed transcripts

    Language:HTML0130

  • kopalgarg/variantviewer

    interactive variant tables for easy filtering

    Language:R0100

  • jhrcook/protein-language-models

    Experimenting with protein language model predictions

    Language:Python10

  • tschmenger/PROTEORIZER

    An explorative tool to identify functional hotspots

    Language:Python10