dohlee / chromoformerLinks
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
☆37Updated 2 years ago
Alternatives and similar repositories for chromoformer
Users that are interested in chromoformer are comparing it to the libraries listed below
Sorting:
- Large language modeling applied to T-cell receptor (TCR) sequences.☆59Updated 3 years ago
- Computational Optimization of DNA Activity (CODA)☆67Updated 10 months ago
- Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.☆142Updated 11 months ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Updated last year
- ☆42Updated last week
- ☆15Updated this week
- surrogate quantitative interpretability for deepnets☆24Updated 5 months ago
- PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation☆61Updated 3 weeks ago
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆191Updated last year
- Contextual AI models for single-cell protein biology☆96Updated 11 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆92Updated 2 months ago
- ☆86Updated 2 years ago
- Benchmarking DNA Language Models on Biologically Meaningful Tasks☆128Updated last year
- Interpretation by Deep Generative Masking for Biological Sequences☆37Updated 4 years ago
- Primary RNA sequence model☆42Updated last year
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆43Updated 7 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆44Updated 2 weeks ago
- Comprehensive suite for evaluating perturbation prediction models☆120Updated 2 weeks ago
- Repository for the paper: "SPACE: STRING proteins as complementary embeddings"☆34Updated 2 months ago
- This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'☆96Updated 2 years ago
- BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity☆60Updated last month
- Deep Learning the T Cell Receptor Binding Specificity of Neoantigen☆89Updated 3 years ago
- ☆79Updated 3 weeks ago
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆121Updated last week
- ☆100Updated 2 months ago
- ☆92Updated 5 months ago
- Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.☆35Updated 6 months ago
- python tools for TCR:peptide-MHC modeling and analysis☆88Updated last year
- ☆19Updated last year
- Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2…☆30Updated 6 months ago