DNA Sequence ML ML Frameworks

Tools for applying machine learning to DNA sequence analysis, prediction, and interpretation. Includes sequence encoding, mutation detection, and sequence-to-function modeling. Does NOT include protein/peptide analysis, chromatin binding prediction, or variant classification.

There are 29 dna sequence ml frameworks tracked. 1 score above 50 (established tier). The highest-rated is helicalAI/helical at 69/100 with 195 stars and 3,330 monthly downloads.

Get all 29 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=ml-frameworks&subcategory=dna-sequence-ml&limit=20"

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#	Framework	Score	Tier	Stars	Language
1	helicalAI/helical A framework for state-of-the-art pre-trained bio foundation models on...	69	Established	195	Python
2	instadeepai/nucleotide-transformer Foundation Models for Genomics & Transcriptomics	48	Emerging	843	Jupyter Notebook
3	ML-Bioinfo-CEITEC/genomic_benchmarks Benchmarks for classification of genomic sequences	47	Emerging	173	Jupyter Notebook
4	FunctionLab/selene a framework for training sequence-level deep learning networks	43	Emerging	398	Jupyter Notebook
5	modernatx/seqlike Unified biological sequence manipulation in Python	42	Emerging	208	Python
6	NetherlandsForensicInstitute/DNANet An open source repository offering tools for parsing DNA profiles and...	40	Emerging	10	Python
7	Future-House/BixBench Benchmark for LLM-based Agents in Computational Biology	37	Emerging	79	Python
8	Lattice-Automation/icor-codon-optimization RNN-based Codon Optimization Tool. Publication:...	36	Emerging	71	Python
9	drivenbyentropy/aptasuite A full-featured bioinformatics software collection for the comprehensive...	34	Emerging	28	Java
10	tanjimin/Chromnitron A multimodal model predicting chromatin-associated proteins binding on the...	31	Emerging	22	Python
11	zhaoweiyu-github/ChromBERT ChromBERT: A pre-trained foundation model for context-specific transcription...	28	Experimental	20	Python
12	carpentries-incubator/rna-seq-data-for-ml RNA-Seq: Data Readiness for Machine Learning Applications	25	Experimental	3	R
13	ML4GLand/SeqPro Genomic sequence preprocessing toolkit	24	Experimental	13	Python
14	ML4GLand/SeqExplainer Interpreting sequence-to-function machine learning models	23	Experimental	6	Jupyter Notebook
15	jang1563/SpaceOmicsBench A multi-omics AI benchmark for spaceflight biomedical data — 21 ML tasks...	22	Experimental	—	Python
16	Devanik21/EternaSeq Bioinformatics pipeline for DNA/RNA sequencing — QC, reference alignment,...	22	Experimental	—	Python
17	jang1563/SpaceOmicsBench-v3 SpaceOmicsBench v3: Multi-mission, multi-omics AI benchmark for spaceflight...	22	Experimental	—	Python
18	arminZolfaghari/DNA-Sequence-Classification Analysis of DNA Sequence Classification Using Neural Networks -...	19	Experimental	19	Jupyter Notebook
19	quantum-lichen/N-Codon-BioAI Official implementation of the N-Codon Protocol. A biomimetic digital...	19	Experimental	—	—
20	NationalGenomicsCenter/eDNAssay This repository contains scripts and data for training and utilizing machine...	18	Experimental	6	R
21	ovitrac/sig2dna 📡🧬 sig2dna: Symbolic transformation of analytical signals into a DNA-like...	17	Experimental	2	Python
22	amirosla/bioseq-platform Multi-service bioinformatics platform for DNA/RNA sequence analysis — Spring...	15	Experimental	1	Java
23	coderfeye13/PatternTermProject Machine learning project classifying left vs right hand DNA traces from...	15	Experimental	1	Python
24	Mvila035/dna_parser A Python module written in rust to encode DNA sequences for machine learning	15	Experimental	7	Rust
25	NaosinLineya/dna-promoter-classification Machine learning pipeline to classify DNA promoter sequences using k-mer features	14	Experimental	—	Jupyter Notebook
26	ML4GLand/SeqData Annotated sequence data	14	Experimental	11	Jupyter Notebook
27	layaasiv/tfbs-classification TFBS classification using k-mer SVM and LS-GKM with motif interpretability...	14	Experimental	—	Jupyter Notebook
28	YashBhadange2006/NanoDNA-Transformer A deep learning based DNA sequence analysis project using an attention model...	13	Experimental	—	Jupyter Notebook
29	bryancastillo10/dna-seq-explorer Web App for Basic Molecular Biology Analysis (with trained AI feature for...	12	Experimental	1	TypeScript

Comparisons in this category

SpaceOmicsBench-v3 and SpaceOmicsBench (22 vs 22)