Foundation Models for Genomics & Transcriptomics
☆848Feb 24, 2026Updated last month
Alternatives and similar repositories for nucleotide-transformer
Users that are interested in nucleotide-transformer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena☆776Apr 22, 2025Updated 11 months ago
- [ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome☆474Jan 1, 2026Updated 3 months ago
- Genomic Pre-trained Network☆337Mar 25, 2026Updated 3 weeks ago
- Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch☆558Jul 7, 2025Updated 9 months ago
- DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome☆750Jan 22, 2026Updated 2 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Biological foundation modeling from molecular to genome scale☆1,497Mar 20, 2026Updated 3 weeks ago
- Benchmarks for classification of genomic sequences☆174Aug 14, 2025Updated 8 months ago
- ☆49Mar 22, 2026Updated 3 weeks ago
- RNA-seq prediction with deep convolutional neural networks.☆235Aug 28, 2025Updated 7 months ago
- [ISMB 2025] DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models☆126Jan 1, 2026Updated 3 months ago
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆320Mar 26, 2026Updated 2 weeks ago
- Computational Optimization of DNA Activity (CODA)☆67Apr 3, 2025Updated last year
- 🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨☆472Mar 25, 2026Updated 3 weeks ago
- code to run sei and obtain sei and sequence class predictions☆113Dec 20, 2022Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Bi-Directional Equivariant Long-Range DNA Sequence Modeling☆230Mar 18, 2026Updated 3 weeks ago
- 🧬 ManyFold: An efficient and flexible library for training and validating protein folding models☆81Dec 14, 2022Updated 3 years ago
- Benchmarking DNA Language Models on Biologically Meaningful Tasks☆129Oct 31, 2024Updated last year
- A Large-Scale Dataset and Framework for Genetic Variant Representation Learning☆33Apr 4, 2026Updated last week
- Biological sequence analysis for the modern age.☆268Feb 22, 2026Updated last month
- Evolutionary Scale Modeling (esm): Pretrained language models for proteins☆4,034Feb 7, 2024Updated 2 years ago
- Genome modeling and design across all domains of life☆3,801Mar 20, 2026Updated 3 weeks ago
- GENA-LM is a transformer masked language model trained on human DNA sequence.☆222Updated this week
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆52Jan 19, 2026Updated 2 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…☆90Dec 10, 2025Updated 4 months ago
- This repository hosts a minimal version of a Python API for BPNet.☆56Jan 24, 2026Updated 2 months ago
- ☆25Jan 9, 2026Updated 3 months ago
- Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them☆179Mar 19, 2026Updated 3 weeks ago
- Nature Methods: RNA foundation model (together with RhoFold)☆362May 27, 2025Updated 10 months ago
- Sequential regulatory activity predictions with deep convolutional neural networks.☆467Jan 15, 2026Updated 3 months ago
- Evaluating genomic sequence models for explaining personalized expression variation☆20Dec 6, 2023Updated 2 years ago
- ☆2,302Mar 19, 2026Updated 3 weeks ago
- ☆25Jun 5, 2025Updated 10 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- deep learning-inspired explainable sequence model for transcription initiation☆103Mar 3, 2025Updated last year
- ☆1,537Nov 12, 2025Updated 5 months ago
- GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics☆143Mar 20, 2026Updated 3 weeks ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆217Feb 2, 2026Updated 2 months ago
- ☆26Nov 7, 2023Updated 2 years ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆73Apr 28, 2023Updated 2 years ago
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆24Jun 26, 2024Updated last year