Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: variant-effect-prediction
gagneurlab/MMSplice_MTSplice
Tissue-specific variant effect predictions on splicing
Language: Jupyter Notebook - Size: 82.3 MB - Last synced: about 13 hours ago - Pushed: 12 months ago - Stars: 38 - Forks: 22
OpenOmics/genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
Language: Python - Size: 919 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 16 - Forks: 7
kkwock/VARify
Transcriptional variant verification to validate predicted variants from genomic data in expressed transcripts
Language: HTML - Size: 48.9 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0
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: 11 days ago - Pushed: about 1 year ago - Stars: 8 - Forks: 1
songlab-cal/gpn
Genomic Pre-trained Network
Language: Jupyter Notebook - Size: 52.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 151 - Forks: 19
allydunham/sequence_unet
Fully convolutional deep learning variant effect predictor architecture
Language: Python - Size: 2.12 MB - Last synced: 12 days ago - Pushed: 4 months ago - Stars: 21 - Forks: 4
DeepRank/DeepRank-Mut 📦
Deep learning framework to predict functional effects of missense variants in human
Language: Python - Size: 187 MB - Last synced: 4 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 0
kircherlab/CADD-SV
CADD-SV – a framework to score the effect of structural variants
Language: Python - Size: 23.2 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 12 - Forks: 3
kopalgarg/variantviewer
interactive variant tables for easy filtering
Language: R - Size: 2 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0
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: 7 months ago - Pushed: over 6 years ago - Stars: 16 - Forks: 1
jhrcook/protein-language-models
Experimenting with protein language model predictions
Language: Python - Size: 3.91 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0
anilprakash94/neur_ally
Deep learning model for non-coding regulatory variants
Language: Python - Size: 4.85 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
CERC-Genomic-Medicine/vep_pipeline
Pipeline for variant annotation using Variant Effect Predictor (VEP)
Language: Jupyter Notebook - Size: 554 KB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 1 - 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: 13 days ago - Pushed: about 1 year 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: 16 days ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
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: about 1 year ago - Pushed: about 3 years ago - Stars: 11 - Forks: 5
allydunham/dms_mutations
Preliminary analysis of a combined DMS dataset, including clustering and VEP benchmark
Language: R - Size: 407 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0