Genomic Variant Analysis ML Frameworks

Tools for predicting variant effects, ancestry inference, gene classification, and genomic element interpretation using neural networks and deep learning. Does NOT include general sequence alignment, peptide design, or non-genetic biomarker prediction.

There are 61 genomic variant analysis frameworks tracked. 3 score above 50 (established tier). The highest-rated is aertslab/CREsted at 61/100 with 57 stars and 72,063 monthly downloads.

Get all 61 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	aertslab/CREsted CREsted is a Python package for training sequence-based deep learning models...	61	Established	57	Python
2	AI-sandbox/gnomix A fast, scalable, and accurate local ancestry method.	55	Established	109	Python
3	BIMSBbioinfo/janggu Deep learning infrastructure for genomics	50	Established	257	Jupyter Notebook
4	kr-colab/ReLERNN Recombination Landscape Estimation using Recurrent Neural Networks	48	Emerging	66	Python
5	arnor-sigurdsson/EIR A toolkit for training deep learning models on genotype, tabular, sequence,...	47	Emerging	42	Python
6	grimmlab/easyPheno easyPheno: a model agnostic phenotype prediction framework	47	Emerging	14	Python
7	kundajelab/dragonn A toolkit to learn how to model and interpret regulatory sequence data using...	42	Emerging	264	Jupyter Notebook
8	gear-genomics/ancient Ancestry inference with convolutional neural networks	40	Emerging	9	Vue
9	krishnanlab/PyGenePlexus A network based gene classification library to generate genome wide...	40	Emerging	20	Python
10	VisualPhysiologyDB/visual-physiology-opsin-db A database of opsin genotype-phenotype data and machine-learning models...	39	Emerging	8	Jupyter Notebook
11	GBeurier/nirs4all A library for Near Infrared Sprectroscopy prediction. NIRS ML. Rebuild of...	39	Emerging	2	Jupyter Notebook
12	databio/geniml Genomic interval machine learning	39	Emerging	21	Python
13	Marijn-Schipper/FLAMES FLAMES: Accurate gene prioritization in GWAS loci	37	Emerging	57	Python
14	ArnovanHilten/GenNet Framework for Interpretable Neural Networks	36	Emerging	115	Jupyter Notebook
15	XMU-Kuangnan-Fang-Team/GENetLib A Python library for Gene–environment interaction analysis via deep learning	35	Emerging	196	Python
16	gaarangoa/pbmf Predictive Biomarker Modeling Framework (PBMF)	33	Emerging	24	Jupyter Notebook
17	usnistgov/lantern Interpretable genotype-phenotype landscape modeling	33	Emerging	36	Python
18	GenomeNet/deepG DeepG, or 'Deep Genomics', is a R library which allows to train and apply...	30	Emerging	28	R
19	CodeByPinar/gen-expression Gene expression analysis is a fundamental component of genomics research,...	28	Experimental	10	Jupyter Notebook
20	JChander/DeepRIG A deep model infers gene regulation networks from scRNA-seq data.	28	Experimental	12	Jupyter Notebook
21	ML4GLand/EUGENe Elucidating the Utility of Genomic Elements with Neural Nets	27	Experimental	69	Jupyter Notebook
22	jst-seminar-rostlab-tum/genomics.ai a web application to annotate and visualise single-cell sequencing data...	27	Experimental	8	JavaScript
23	rayanebelhadj/BiomeML Classification de maladies par microbiome avec des reseaux de neurones sur...	25	Experimental	4	Jupyter Notebook
24	PathoGenOmics-Lab/pathotypr Genome classificator using machine learning and SNP markers.	25	Experimental	3	JavaScript
25	dyneth02/Genome-based-Disorder-Prediction-System Machine learning system for predicting genetic disorders using genomic,...	24	Experimental	11	JavaScript
26	NicholasDominic/The-NucleoNets A novel deep polygenic neural network for predicting and identifying...	24	Experimental	3	Python
27	nec-research/microbiome-mvib Microbiome-based disease prediction with multimodal variational information...	23	Experimental	25	Python
28	uri0l/metabolomics_sex_differences A bioinformatics pipeline in R to identify sex-associated biomarkers in the...	23	Experimental	1	—
29	tathadn/gut-microbiome-disease-classifier Multi-disease gut microbiome classifier using CLR-transformed OTU profiles,...	22	Experimental	—	Jupyter Notebook
30	Niza46/SYNGAP1-Variant-Viewer 🧬 Visualize SYNGAP1 genetic variants interactively with this R Shiny app,...	22	Experimental	—	R
31	sabowler/bioml Binary classification toolkit for biomedical ML (SVM, XGBoost, KNN, and NN)...	22	Experimental	—	Python
32	mmeridius544-cyber/Genetics-Influence-On-pschiatric-deceases this project implements a computational pipeline for modelling genetic risk...	22	Experimental	—	Jupyter Notebook
33	LA777am/GenoScope_pl GenoScope is a full-stack computational genomics platform built with Flask,...	22	Experimental	—	HTML
34	finnX228/Gengram 🧬 Enhance genomic understanding with Gengram, a conditional memory module...	22	Experimental	—	Python
35	Elliot-Chan-120/GEM GEM \| Gene Edit Machine: A machine learning-enhanced platform capable of...	22	Experimental	—	Python
36	adamavip/nirs-protein-prediction We present here a 1D convolutional neural network model to predict grain...	21	Experimental	14	Jupyter Notebook
37	BiomedSciAI/Geno4SD An python omics data toolkit for the analysis across biological scales	21	Experimental	11	Jupyter Notebook
38	NAMlab/DeepCRE Deep learning the cis-regulatory code for gene expression in selected model plants	21	Experimental	23	R
39	adamavip/fatty_acid_nirs_model Using near-infrared spectroscopy (NIRS) and machine learning to determine...	20	Experimental	12	Python
40	dyneth02/FDM-Labs Comprehensive machine learning framework for genomic analysis and predictive...	19	Experimental	8	Jupyter Notebook
41	C0nc/River A Python package for identification Differential Spatial Expression Pattern...	18	Experimental	7	Jupyter Notebook
42	AlvaroTorresMartos/IR_prediction This is an online repository gathering all codes employed for the analyses...	18	Experimental	3	R
43	dDipankar/DeepGuide DeepGuide: a tool to predict CRIPR activity	16	Experimental	4	MATLAB
44	HemantBatra873/CRISPRight CRISPRight is a research-driven deep learning project that analyzes...	15	Experimental	—	Python
45	Zhihan-Leo-Liu/DosaCNV Deep multiple instance learning model for predicting deletion pathogenicity...	15	Experimental	2	R
46	hanchen9127/GeneAnalysis An R Shiny APP for analyzing and visualizing the association between gene...	15	Experimental	—	HTML
47	SWi1/diet_PUP_relationships Analysis scripts for the comparison of dietary polyphenol intake and...	15	Experimental	—	R
48	systems-genomics-lab-auc/systems-genomics-lab.github.io data analytics & machine learning meet genetics @ AUC	15	Experimental	—	JavaScript
49	Ragerlab/2021_Clark_et_al_Comparing-the-Predictivity-of-Human-Placental-Gene-microRNA-and-CpG-Methylation Script that associates with: ‘Comparing the Predictivity of Human Placental...	14	Experimental	—	R
50	NaealApp/FDM-Labs 🧬 Analyze genomic data and build predictive models for genetic disorders...	14	Experimental	—	C++
51	Ragerlab/2021_Clark_Comparing-the-Predictivity-of-Human-Placental-Gene-microRNA-and-CpG-Methylation-Signatu Script that associates with: ‘Comparing the Predictivity of Human Placental...	14	Experimental	—	R
52	WevertonGomesCosta/Integrating-nir-genomic-kernel Demonstrar que a fusão de dados espectrais e genômicos pode aumentar...	14	Experimental	—	R
53	Yedomon/bravo_project Transcriptome analysis of oilseed rape genotypes	14	Experimental	—	R
54	milesroberts-123/slim-sweep-cnn A workflow to simulate selective sweeps in SLiM and turn the results into images	14	Experimental	—	Python
55	GuLinLin/ELPGV Ensemble learning for integrative prediction of genetic values with genomic variants.	12	Experimental	3	R
56	anilprakash94/neur_ally Deep learning model for non-coding regulatory variants	12	Experimental	1	Python
57	climatechangemicrobiology/ProGRN Prokaryote Gene Regulatory Network (ProGRN) Inference Pipeline	11	Experimental	2	HTML
58	ogrecio/GenomeWidePrediction_course GENOME-WIDE PREDICTION OF COMPLEX TRAITS IN HUMANS, PLANTS AND ANIMALS	11	Experimental	2	R
59	ZheFrench/Omics Omics : Feel free to contact me if you want I give a hand to analyze your data !	11	Experimental	—	JavaScript
60	chhuang216/gene-expression-ai-pipeline End-to-end ML/AI pipeline for gene-expression prediction & explainability	11	Experimental	—	Jupyter Notebook
61	bchryzal/Genome-sequence-undergoing-mutation Predict the likelihood of a genome sequence undergoing mutation.	10	Experimental	1	Jupyter Notebook