castillohair / paper-5utr-design
Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"
☆17Updated 7 months ago
Alternatives and similar repositories for paper-5utr-design:
Users that are interested in paper-5utr-design are comparing it to the libraries listed below
- Modeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.☆44Updated 5 years ago
- Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor☆44Updated 6 months ago
- ☆26Updated last month
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆35Updated 3 weeks ago
- ☆71Updated last year
- Computational Optimization of DNA Activity (CODA)☆55Updated last month
- STAPLER (Shared TCR And Peptide Language bidirectional Encoder Representations from transformers) is a language model that uses a joint T…☆25Updated 9 months ago
- 🧛 Deep generative models for TCR sequences 🧛☆17Updated 2 years ago
- HLA-II ligand predictor.☆39Updated last year
- ☆17Updated 10 months ago
- ScanFold is an RNA sequence scanning pipeline which attempts to identify potentially functional RNA secondary structures. This is done by…☆17Updated 2 years ago
- ERGO is a deep learing based model for predicting TCR-peptide binding.☆17Updated 2 years ago
- ☆73Updated 4 months ago
- Generic TCR-epitope recognition prediction using CNN approach on both known and novel epitopes☆15Updated last year
- Interpretation by Deep Generative Masking for Biological Sequences☆37Updated 3 years ago
- Code for 5UTR project☆24Updated last year
- python tools for TCR:peptide-MHC modeling and analysis☆69Updated 10 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆35Updated 2 months ago
- Promoter activity measurement and modeling; artificial promoter design and testing☆12Updated last year
- a framework for predicting global protein-protein interaction networks from dynamic mass spec data☆23Updated 10 months ago
- HLA-I ligand predictor☆32Updated last month
- ☆37Updated last year
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆34Updated 3 months ago
- NetTCR-2.0. Sequence-based prediction of peptide-TCR binding☆33Updated 2 years ago
- Large language modeling applied to T-cell receptor (TCR) sequences.☆49Updated 2 years ago
- APA Regression Net - Predict and Engineer Alternative Polyadenylation☆39Updated 3 years ago
- ERGO-II, an updated version of ERGO including more features for TCR-peptide binding prediction☆29Updated 2 years ago
- Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".☆57Updated 3 years ago
- Knowledge-primed neural networks☆35Updated last year
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆36Updated 4 months ago