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. 4 score above 50 (established tier). The highest-rated is helicalAI/helical at 65/100 with 195 stars.

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...	65	Established	195	Python
2	instadeepai/nucleotide-transformer Foundation Models for Genomics & Transcriptomics	55	Established	843	Jupyter Notebook
3	ML-Bioinfo-CEITEC/genomic_benchmarks Benchmarks for classification of genomic sequences	54	Established	173	Jupyter Notebook
4	FunctionLab/selene a framework for training sequence-level deep learning networks	50	Established	398	Jupyter Notebook
5	modernatx/seqlike Unified biological sequence manipulation in Python	49	Emerging	208	Python
6	Future-House/BixBench Benchmark for LLM-based Agents in Computational Biology	44	Emerging	79	Python
7	Lattice-Automation/icor-codon-optimization RNN-based Codon Optimization Tool. Publication:...	43	Emerging	71	Python
8	NetherlandsForensicInstitute/DNANet An open source repository offering tools for parsing DNA profiles and...	43	Emerging	10	Python
9	drivenbyentropy/aptasuite A full-featured bioinformatics software collection for the comprehensive...	41	Emerging	28	Java
10	tanjimin/Chromnitron A multimodal model predicting chromatin-associated proteins binding on the...	37	Emerging	22	Python
11	zhaoweiyu-github/ChromBERT ChromBERT: A pre-trained foundation model for context-specific transcription...	35	Emerging	20	Python
12	carpentries-incubator/rna-seq-data-for-ml RNA-Seq: Data Readiness for Machine Learning Applications	32	Emerging	3	R
13	ML4GLand/SeqPro Genomic sequence preprocessing toolkit	31	Emerging	13	Python
14	ML4GLand/SeqExplainer Interpreting sequence-to-function machine learning models	30	Emerging	6	Jupyter Notebook
15	arminZolfaghari/DNA-Sequence-Classification Analysis of DNA Sequence Classification Using Neural Networks -...	26	Experimental	19	Jupyter Notebook
16	NationalGenomicsCenter/eDNAssay This repository contains scripts and data for training and utilizing machine...	25	Experimental	6	R
17	ovitrac/sig2dna 📡🧬 sig2dna: Symbolic transformation of analytical signals into a DNA-like...	23	Experimental	2	Python
18	jang1563/SpaceOmicsBench-v3 SpaceOmicsBench v3: Multi-mission, multi-omics AI benchmark for spaceflight...	22	Experimental	—	Python
19	Devanik21/EternaSeq Bioinformatics pipeline for DNA/RNA sequencing — QC, reference alignment,...	22	Experimental	—	Python
20	Mvila035/dna_parser A Python module written in rust to encode DNA sequences for machine learning	22	Experimental	7	Rust
21	jang1563/SpaceOmicsBench A multi-omics AI benchmark for spaceflight biomedical data — 21 ML tasks...	22	Experimental	—	Python
22	ML4GLand/SeqData Annotated sequence data	21	Experimental	11	Jupyter Notebook
23	coderfeye13/PatternTermProject Machine learning project classifying left vs right hand DNA traces from...	19	Experimental	1	Python
24	YashBhadange2006/NanoDNA-Transformer A deep learning based DNA sequence analysis project using an attention model...	15	Experimental	—	Jupyter Notebook
25	amirosla/bioseq-platform Multi-service bioinformatics platform for DNA/RNA sequence analysis — Spring...	14	Experimental	1	Java
26	layaasiv/tfbs-classification TFBS classification using k-mer SVM and LS-GKM with motif interpretability...	11	Experimental	—	Jupyter Notebook
27	Syedkumailhaider512/TrueDNA TrueDNA is a comprehensive and powerful computational biology project...	11	Experimental	—	Python
28	NaosinLineya/dna-promoter-classification Machine learning pipeline to classify DNA promoter sequences using k-mer features	11	Experimental	—	Jupyter Notebook
29	vaniseth/DNA-Classifier-and-Comparator Testing DNA sequences against various classification allgorithms	10	Experimental	2	Jupyter Notebook