variant-effect-prediction

There are 0 repository under variant-effect-prediction topic.

songlab-cal / gpn
Genomic Pre-trained Network
dna language-model variant-effect-prediction
Language:Jupyter Notebook 165
gagneurlab / MMSplice_MTSplice
Tissue-specific variant effect predictions on splicing
machine-learning splicing variant-effect-prediction vep-plugin
Language:Jupyter Notebook 39
allydunham / sequence_unet
Fully convolutional deep learning variant effect predictor architecture
deep-learning convolutional-neural-networks variant-effect-prediction unet
Language:Python 22
elaspic / elaspic2
Predicting the effect of mutations on protein stability and protein binding affinity using pretrained neural networks and a ranking objective function.
mutations protein-structure protein-stability binding-affinity variant-effect-prediction protein bioinformatics
Language:Jupyter Notebook 18
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/.
envision2017 variant-effect-prediction machine-learning
Language:Jupyter Notebook 16
OpenOmics / genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
copy-number-variation germline-variants quality-control structural-variants singularity snakemake whole-genome-sequencing somatic-variants pipeline hla-typing variant-annotation variant-effect-prediction whole-exome-sequencing
Language:Python 16
kircherlab / CADD-SV
CADD-SV – a framework to score the effect of structural variants
sv variant-annotations variant-effect-prediction
Language:Python 14
dohlee / spliceai-pytorch
Implementation of SpliceAI, Illumina's deep neural network to predict variant effects on splicing, in PyTorch.
artificial-intelligence bioinformatics biology computational-biology deep-learning deep-neural-networks reproduction reproduction-code splicing variant-effect-prediction
Language:Jupyter Notebook 10
CERC-Genomic-Medicine / vep_pipeline
Pipeline for variant annotation using Variant Effect Predictor (VEP)
genetics variant-annotation pipeline annotations variant nextflow vep-annotation gwas variant-effect-prediction vep
Language:Jupyter Notebook 4
allydunham / dms_mutations
Preliminary analysis of a combined DMS dataset, including clustering and VEP benchmark
deep-mutational-scanning variant-effect-prediction benchmark
Language:R 1
anilprakash94 / neur_ally
Deep learning model for non-coding regulatory variants
artificial-intelligence attention-network deep-learning genomics neurological noncoding-mutations regulatory-genomics variant-effect-prediction
Language:Python 1
DeepRank / DeepRank-Mut
Deep learning framework to predict functional effects of missense variants in human
missense-mutations variant-effect-prediction 3dcnn protein-structure
Language:Python 1
dohlee / eve-pytorch
Implementation of evolutionary model of variant effect (EVE), a deep generative model of evolutionary data, in PyTorch.
bioinformatics computational-biology evolution variant-effect-prediction variational-autoencoder biology deep-learning reproduction reproduction-code
Language:Python 1
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.
haskell parsing ensembl-vep composable unix-tool variant-effect-prediction variant-call-format vcf-converter
Language:Haskell 1
kkwock / VARify
Transcriptional variant verification to validate predicted variants from genomic data in expressed transcripts
rna-seq variant-effect-prediction wes wgs
Language:HTML 0
kopalgarg / variantviewer
interactive variant tables for easy filtering
variant-annotations variant-effect-prediction variant-calling shinydashboard
Language:R 0
jhrcook / protein-language-models
Experimenting with protein language model predictions
data-analysis protein-language-model variant-effect-prediction
Language:Python

variant-effect-prediction

songlab-cal / gpn

gagneurlab / MMSplice_MTSplice

allydunham / sequence_unet

elaspic / elaspic2

FowlerLab / Envision2017

OpenOmics / genome-seek

kircherlab / CADD-SV

dohlee / spliceai-pytorch

CERC-Genomic-Medicine / vep_pipeline

allydunham / dms_mutations

anilprakash94 / neur_ally

DeepRank / DeepRank-Mut

dohlee / eve-pytorch

Matthew-Mosior / Basic-Variant-Parser

kkwock / VARify

kopalgarg / variantviewer

jhrcook / protein-language-models