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 48 rna structure learning frameworks tracked. 5 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 48 projects as JSON

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

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#	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.	57	Established	45	Python
3	google/deepsomatic DeepSomatic is an analysis pipeline that uses a deep neural network to call...	56	Established	296	—
4	Kuanhao-Chao/OpenSpliceAI 🤖 Open‑source deep-learning-based splice‑site predictor that decodes...	55	Established	40	Python
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	48	Emerging	53	Python
7	Tom-Ellis-Lab/yorzoi RNA-seq coverage prediction from DNA sequence in Yeast	48	Emerging	6	Jupyter Notebook
8	HKU-BAL/ClairS ClairS - a deep-learning method for long-read somatic small variant calling	47	Emerging	105	Python
9	cauliyang/DeepBioP Deep Learning Processing Library for Biological Data	45	Emerging	5	Rust
10	HKU-BAL/Clair3 Clair3 - Symphonizing pileup and full-alignment for deep learning-based...	44	Emerging	343	Python
11	HKU-BAL/Clair3-RNA Clair3-RNA - a long-read small variant caller for RNA sequencing data	43	Emerging	40	Python
12	JelenaBanjac/microbiome-toolbox Early Life Microbiome Toolbox	41	Emerging	12	Jupyter Notebook
13	kaist-ina/BWA-MEME BWA-MEME: Faster BWA-MEM2 using learned-index	40	Emerging	133	C++
14	simonorozcoarias/Inpactor2 Inpactor2: LTR retrotransposon detector and classificator using Deep Learning	39	Emerging	28	Jupyter Notebook
15	liyu95/DeepSimulator The first deep learning based Nanopore simulator which can simulate the...	39	Emerging	123	C
16	HKU-BAL/ClairS-TO ClairS-TO - a deep-learning method for tumor-only somatic variant calling	38	Emerging	82	Python
17	leylabmpi/resmico Identifying misassemblies via deep learning	37	Emerging	11	Jupyter Notebook
18	dohlee/spliceai-pytorch Implementation of SpliceAI, Illumina's deep neural network to predict...	37	Emerging	15	Jupyter Notebook
19	ChaorongC/mesa_cfdna A flexible and sensitive method for capturing and integrating multimodal...	37	Emerging	2	Jupyter Notebook
20	comprna/CHEUI Concurrent identification of m6A and m5C modifications in individual...	34	Emerging	44	C++
21	WGLab/DeepMod2 DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads	33	Emerging	61	Jupyter Notebook
22	vadanamu/DeepRM Deep learning for RNA Modification	30	Emerging	6	C
23	fpozoc/trifid Machine Learning-based tool to assess the functional relevance of splice isoforms.	27	Experimental	12	Python
24	raghavagps/emirpred EmiRPred: A computational approach to predict exosomal and non-exosomal miRNA	26	Experimental	1	Python
25	lizhao007/DeepBSA DeepBSA is a novel bulked segregant analysis (BSA) software for the...	25	Experimental	22	—
26	ke-laboratory/iM6A Modeling m6A site-specific deposition by iM6A	25	Experimental	6	Jupyter Notebook
27	Kuanhao-Chao/splam ✂️ Deep learning-based splice site predictor that improves spliced alignments	25	Experimental	59	C++
28	Naila-Srivastava/AI-Powered-Variant-Prioritisation-RareDiseases Extending WES variant calling with ML to intelligently prioritise VUS for...	24	Experimental	1	Jupyter Notebook
29	OluwadareLab/EnsembleSplice Ensemble Deep Learning for Splice Site Prediction	24	Experimental	4	PureBasic
30	GuglielmoCerri/mRNA-degradation-prediction A deep learning model predicting mRNA degradation rates based on the...	23	Experimental	3	Jupyter Notebook
31	sablokrep/antimicrotransform microbial transformers	21	Experimental	—	Rust
32	sablokrep/biomeML entire machine learning for microbime	21	Experimental	—	Rust
33	sablokrep/beesag a bee genome resource	21	Experimental	—	Rust
34	sablokrep/beemorph morphological diversity bees	21	Experimental	—	Rust
35	brentp/spacepile convert reads from repeated measures of same piece of DNA into spaced...	21	Experimental	14	Rust
36	sablokrep/beesmile a QSAR modelling of chemical structures	21	Experimental	—	Rust
37	sablokrep/seqboost graph neural network	21	Experimental	—	Rust
38	adhiraj141092/RNAinsecta RNAinsecta: A tool for prediction of pre-microRNA in insects using machine...	19	Experimental	3	C
39	sablokrep/toxannotator rustic tox annotator for comparative genomics	17	Experimental	—	Rust
40	sablokrep/rnaml prepairing rna predictions for deep learning	17	Experimental	—	Rust
41	sablokrep/protalignspec alignment to spectral intensities for deep learning	17	Experimental	—	Rust
42	sablokrep/varpred a variant count approach to predict variant	17	Experimental	—	Rust
43	aarati0505/rRNA-NOR-pipeline A machine learning pipeline for comparative analysis of 45S rRNA genes from...	14	Experimental	—	Python
44	dianalaplace/scoliosis-variant-ml ML pipeline for pathogenic variant analysis in scoliosis genes using...	14	Experimental	—	Python
45	DavidF-22/ICS3909-FYP This repository contains the codebase for a final year project focused on...	13	Experimental	3	Python
46	cbl-nabi/RNAChallenge RNAchallenge dataset for the classification of protein-coding and non-coding RNAs	12	Experimental	5	—
47	comprna/CHEUI-public Concurrent identification of m6A and m5C modifications in individual...	12	Experimental	1	—
48	hrydbeck/PLmicRO Machine learning for microbiology — reading list, literature curation with...	11	Experimental	—	Python

Comparisons in this category

ClairS and Clair3 (47 vs 44) Clair3 and Clair3-RNA (44 vs 43) ClairS and ClairS-TO (47 vs 38) ClairS and Clair3-RNA (47 vs 43)