RNA Structure Learning ML Frameworks

Tools for applying deep learning to RNA sequences and structures, including alignment, prediction, and graph-based representations of RNA molecules. Does NOT include general sequence alignment, peptide/protein folding, or non-ML bioinformatics tools.

There are 52 rna structure learning frameworks tracked. 7 score above 50 (established tier). The highest-rated is google/deepvariant at 64/100 with 3,654 stars. 1 of the top 10 are actively maintained.

Get all 52 projects as JSON

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

Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.

#	Framework	Score	Tier	Stars	Language
1	google/deepvariant DeepVariant is an analysis pipeline that uses a deep neural network to call...	64	Established	3,654	Python
2	cgoliver/rnaglib Toolkit for structure-based deep learning on RNA.	63	Established	45	Python
3	Kuanhao-Chao/OpenSpliceAI 🤖 Open‑source deep-learning-based splice‑site predictor that decodes...	61	Established	40	Python
4	google/deepsomatic DeepSomatic is an analysis pipeline that uses a deep neural network to call...	56	Established	296	—
5	Merck/deepbgc BGC Detection and Classification Using Deep Learning	54	Established	156	Jupyter Notebook
6	Sanofi-Public/RiboNN RiboNN: predicting translation efficiencies from mRNA sequences	52	Established	53	Python
7	HKU-BAL/ClairS ClairS - a deep-learning method for long-read somatic small variant calling	50	Established	105	Python
8	Tom-Ellis-Lab/yorzoi RNA-seq coverage prediction from DNA sequence in Yeast	48	Emerging	6	Jupyter Notebook
9	HKU-BAL/Clair3 Clair3 - Symphonizing pileup and full-alignment for deep learning-based...	47	Emerging	343	Python
10	HKU-BAL/Clair3-RNA Clair3-RNA - a long-read small variant caller for RNA sequencing data	43	Emerging	40	Python
11	kaist-ina/BWA-MEME BWA-MEME: Faster BWA-MEM2 using learned-index	40	Emerging	133	C++
12	liyu95/DeepSimulator The first deep learning based Nanopore simulator which can simulate the...	39	Emerging	123	C
13	cauliyang/DeepBioP Deep Learning Processing Library for Biological Data	38	Emerging	5	Rust
14	ChaorongC/mesa_cfdna A flexible and sensitive method for capturing and integrating multimodal...	38	Emerging	2	Jupyter Notebook
15	JelenaBanjac/microbiome-toolbox Early Life Microbiome Toolbox	38	Emerging	12	Jupyter Notebook
16	HKU-BAL/ClairS-TO ClairS-TO - a deep-learning method for tumor-only somatic variant calling	38	Emerging	82	Python
17	comprna/CHEUI Concurrent identification of m6A and m5C modifications in individual...	34	Emerging	44	C++
18	leylabmpi/resmico Identifying misassemblies via deep learning	34	Emerging	11	Jupyter Notebook
19	WGLab/DeepMod2 DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads	33	Emerging	61	Jupyter Notebook
20	dohlee/spliceai-pytorch Implementation of SpliceAI, Illumina's deep neural network to predict...	33	Emerging	15	Jupyter Notebook
21	simonorozcoarias/Inpactor2 Inpactor2: LTR retrotransposon detector and classificator using Deep Learning	32	Emerging	28	Jupyter Notebook
22	ylab-hi/DeepChopper Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing	32	Emerging	7	Rust
23	pgrady1322/strandweaver StrandWeaver is an AI/ML-powered genome assembler that combines...	29	Experimental	1	Python
24	vadanamu/DeepRM Deep learning for RNA Modification	26	Experimental	6	C
25	Kuanhao-Chao/splam ✂️ Deep learning-based splice site predictor that improves spliced alignments	25	Experimental	59	C++
26	YichengTuLab/DeepReadMapper Deep learning-based gene alignmer that uses vector similarity search to...	25	Experimental	1	C++
27	sablokrep/beesmile a QSAR modelling of chemical structures	22	Experimental	—	Rust
28	raghavagps/emirpred EmiRPred: A computational approach to predict exosomal and non-exosomal miRNA	22	Experimental	1	Python
29	fpozoc/trifid Machine Learning-based tool to assess the functional relevance of splice isoforms.	20	Experimental	12	Python
30	Naila-Srivastava/AI-Powered-Variant-Prioritisation-RareDiseases Extending WES variant calling with ML to intelligently prioritise VUS for...	20	Experimental	1	Jupyter Notebook
31	sablokrep/varpred a variant count approach to predict variant	19	Experimental	—	Rust
32	sablokrep/biomeML entire machine learning for microbime	19	Experimental	—	Rust
33	sablokrep/beesag a bee genome resource	19	Experimental	—	Rust
34	sablokrep/beemorph morphological diversity bees	19	Experimental	—	Rust
35	sablokrep/antimicrotransform microbial transformers	19	Experimental	—	Rust
36	sablokrep/seqboost graph neural network	19	Experimental	—	Rust
37	sablokrep/graphqlvar a variant graphql server for deep learning.	19	Experimental	—	Rust
38	sablokrep/beechem chemical modelling of bee glues	19	Experimental	—	Rust
39	ke-laboratory/iM6A Modeling m6A site-specific deposition by iM6A	18	Experimental	6	Jupyter Notebook
40	lizhao007/DeepBSA DeepBSA is a novel bulked segregant analysis (BSA) software for the...	18	Experimental	22	—
41	OluwadareLab/EnsembleSplice Ensemble Deep Learning for Splice Site Prediction	17	Experimental	4	PureBasic
42	GuglielmoCerri/mRNA-degradation-prediction A deep learning model predicting mRNA degradation rates based on the...	16	Experimental	3	Jupyter Notebook
43	sablokrep/rnaml prepairing rna predictions for deep learning	15	Experimental	—	Rust
44	sablokrep/protalignspec alignment to spectral intensities for deep learning	15	Experimental	—	Rust
45	sablokrep/toxannotator rustic tox annotator for comparative genomics	15	Experimental	—	Rust
46	dianalaplace/scoliosis-variant-ml ML pipeline for pathogenic variant analysis in scoliosis genes using...	14	Experimental	—	Python
47	hrydbeck/PLmicRO Machine learning for microbiology — reading list, literature curation with...	14	Experimental	—	Python
48	brentp/spacepile convert reads from repeated measures of same piece of DNA into spaced...	14	Experimental	14	Rust
49	aarati0505/rRNA-NOR-pipeline A machine learning pipeline for comparative analysis of 45S rRNA genes from...	14	Experimental	—	Python
50	adhiraj141092/RNAinsecta RNAinsecta: A tool for prediction of pre-microRNA in insects using machine...	12	Experimental	3	C
51	APalaniaLab/RiboSense A web interface for annotating riboswitches in genomic sequences	11	Experimental	—	Vue
52	comprna/CHEUI-public Concurrent identification of m6A and m5C modifications in individual...	10	Experimental	1	—

Comparisons in this category

ClairS and Clair3 (50 vs 47) Clair3 and Clair3-RNA (47 vs 43) ClairS and ClairS-TO (50 vs 38) ClairS and Clair3-RNA (50 vs 43)