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. 6 score above 50 (established tier). The highest-rated is AI-sandbox/gnomix at 62/100 with 109 stars.

Get all 61 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	AI-sandbox/gnomix A fast, scalable, and accurate local ancestry method.	62	Established	109	Python
2	aertslab/CREsted CREsted is a Python package for training sequence-based deep learning models...	58	Established	57	Python
3	kr-colab/ReLERNN Recombination Landscape Estimation using Recurrent Neural Networks	55	Established	66	Python
4	BIMSBbioinfo/janggu Deep learning infrastructure for genomics	53	Established	257	Jupyter Notebook
5	arnor-sigurdsson/EIR A toolkit for training deep learning models on genotype, tabular, sequence,...	51	Established	42	Python
6	grimmlab/easyPheno easyPheno: a model agnostic phenotype prediction framework	51	Established	14	Python
7	kundajelab/dragonn A toolkit to learn how to model and interpret regulatory sequence data using...	49	Emerging	264	Jupyter Notebook
8	gear-genomics/ancient Ancestry inference with convolutional neural networks	47	Emerging	9	Vue
9	Marijn-Schipper/FLAMES FLAMES: Accurate gene prioritization in GWAS loci	44	Emerging	57	Python
10	krishnanlab/PyGenePlexus A network based gene classification library to generate genome wide...	44	Emerging	20	Python
11	databio/geniml Genomic interval machine learning	43	Emerging	21	Python
12	ArnovanHilten/GenNet Framework for Interpretable Neural Networks	43	Emerging	115	Jupyter Notebook
13	VisualPhysiologyDB/visual-physiology-opsin-db A database of opsin genotype-phenotype data and machine-learning models...	43	Emerging	8	Jupyter Notebook
14	XMU-Kuangnan-Fang-Team/GENetLib A Python library for Gene–environment interaction analysis via deep learning	42	Emerging	196	Python
15	usnistgov/lantern Interpretable genotype-phenotype landscape modeling	40	Emerging	36	Python
16	gaarangoa/pbmf Predictive Biomarker Modeling Framework (PBMF)	40	Emerging	24	Jupyter Notebook
17	GenomeNet/deepG DeepG, or 'Deep Genomics', is a R library which allows to train and apply...	37	Emerging	28	R
18	GBeurier/nirs4all A library for Near Infrared Sprectroscopy prediction. NIRS ML. Rebuild of...	37	Emerging	2	Jupyter Notebook
19	JChander/DeepRIG A deep model infers gene regulation networks from scRNA-seq data.	35	Emerging	12	Jupyter Notebook
20	CodeByPinar/gen-expression Gene expression analysis is a fundamental component of genomics research,...	35	Emerging	10	Jupyter Notebook
21	jst-seminar-rostlab-tum/genomics.ai a web application to annotate and visualise single-cell sequencing data...	34	Emerging	8	JavaScript
22	ML4GLand/EUGENe Elucidating the Utility of Genomic Elements with Neural Nets	34	Emerging	69	Jupyter Notebook
23	PathoGenOmics-Lab/pathotypr Genome classificator using machine learning and SNP markers.	32	Emerging	3	JavaScript
24	NicholasDominic/The-NucleoNets A novel deep polygenic neural network for predicting and identifying...	31	Emerging	3	Python
25	dyneth02/Genome-based-Disorder-Prediction-System Machine learning system for predicting genetic disorders using genomic,...	30	Emerging	11	JavaScript
26	nec-research/microbiome-mvib Microbiome-based disease prediction with multimodal variational information...	30	Emerging	25	Python
27	adamavip/nirs-protein-prediction We present here a 1D convolutional neural network model to predict grain...	28	Experimental	14	Jupyter Notebook
28	BiomedSciAI/Geno4SD An python omics data toolkit for the analysis across biological scales	28	Experimental	11	Jupyter Notebook
29	NAMlab/DeepCRE Deep learning the cis-regulatory code for gene expression in selected model plants	28	Experimental	23	R
30	adamavip/fatty_acid_nirs_model Using near-infrared spectroscopy (NIRS) and machine learning to determine...	27	Experimental	12	Python
31	rayanebelhadj/BiomeML Classification de maladies par microbiome avec des reseaux de neurones sur...	26	Experimental	4	Jupyter Notebook
32	AlvaroTorresMartos/IR_prediction This is an online repository gathering all codes employed for the analyses...	25	Experimental	3	R
33	C0nc/River A Python package for identification Differential Spatial Expression Pattern...	25	Experimental	7	Jupyter Notebook
34	dDipankar/DeepGuide DeepGuide: a tool to predict CRIPR activity	23	Experimental	4	MATLAB
35	dyneth02/FDM-Labs Comprehensive machine learning framework for genomic analysis and predictive...	23	Experimental	8	Jupyter Notebook
36	uri0l/metabolomics_sex_differences A bioinformatics pipeline in R to identify sex-associated biomarkers in the...	23	Experimental	1	—
37	tathadn/gut-microbiome-disease-classifier Multi-disease gut microbiome classifier using CLR-transformed OTU profiles,...	22	Experimental	—	Jupyter Notebook
38	sabowler/bioml Binary classification toolkit for biomedical ML (SVM, XGBoost, KNN, and NN)...	22	Experimental	—	Python
39	mmeridius544-cyber/Genetics-Influence-On-pschiatric-deceases this project implements a computational pipeline for modelling genetic risk...	22	Experimental	—	Jupyter Notebook
40	Zhihan-Leo-Liu/DosaCNV Deep multiple instance learning model for predicting deletion pathogenicity...	22	Experimental	2	R
41	finnX228/Gengram 🧬 Enhance genomic understanding with Gengram, a conditional memory module...	22	Experimental	—	Python
42	anilprakash94/neur_ally Deep learning model for non-coding regulatory variants	19	Experimental	1	Python
43	GuLinLin/ELPGV Ensemble learning for integrative prediction of genetic values with genomic variants.	19	Experimental	3	R
44	climatechangemicrobiology/ProGRN Prokaryote Gene Regulatory Network (ProGRN) Inference Pipeline	18	Experimental	2	HTML
45	ogrecio/GenomeWidePrediction_course GENOME-WIDE PREDICTION OF COMPLEX TRAITS IN HUMANS, PLANTS AND ANIMALS	18	Experimental	2	R
46	HemantBatra873/CRISPRight CRISPRight is a research-driven deep learning project that analyzes...	17	Experimental	—	Python
47	systems-genomics-lab-auc/systems-genomics-lab.github.io data analytics & machine learning meet genetics @ AUC	17	Experimental	—	JavaScript
48	bchryzal/Genome-sequence-undergoing-mutation Predict the likelihood of a genome sequence undergoing mutation.	17	Experimental	1	Jupyter Notebook
49	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
50	WevertonGomesCosta/Integrating-nir-genomic-kernel Demonstrar que a fusão de dados espectrais e genômicos pode aumentar...	14	Experimental	—	R
51	MuhammadMuneeb007/EFGPP Exploratory Framework for Genotype-Phenotype Prediction	14	Experimental	6	Python
52	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
53	milesroberts-123/slim-sweep-cnn A workflow to simulate selective sweeps in SLiM and turn the results into images	14	Experimental	—	Python
54	ZheFrench/Omics Omics : Feel free to contact me if you want I give a hand to analyze your data !	13	Experimental	—	JavaScript
55	NaealApp/FDM-Labs 🧬 Analyze genomic data and build predictive models for genetic disorders...	13	Experimental	—	C++
56	SWi1/diet_PUP_relationships Analysis scripts for the comparison of dietary polyphenol intake and...	13	Experimental	—	R
57	GenomeNet/Self-GenomeNet A method that utilizes unlabeled genomic data to address the challenge of...	12	Experimental	8	R
58	Yedomon/bravo_project Transcriptome analysis of oilseed rape genotypes	11	Experimental	—	R
59	FloFlo93/PICA-to-go Phenotype prediction pipeline	11	Experimental	—	Java
60	kenan-erol/MicrobeClassification Classification model predicting the type of microbe from provided features	11	Experimental	—	Jupyter Notebook
61	yebigithub/GBLUP4Met Role of genomics on regulating rice grain metabolic variability under warmer...	11	Experimental	3	R