jmschrei / ledidi
Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
☆72Updated 2 weeks ago
Alternatives and similar repositories for ledidi:
Users that are interested in ledidi are comparing it to the libraries listed below
- Jax code for functional genomics ML☆12Updated last month
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆35Updated 6 months ago
- Machine learning methods for DNA sequence analysis.☆41Updated last week
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆38Updated 6 months ago
- Diverse Genomic Embedding Benchmark☆45Updated last month
- Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…☆61Updated 3 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆46Updated 2 weeks ago
- Interpretable genotype-phenotype landscape modeling☆35Updated last year
- Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors☆40Updated 11 months ago
- RNA-seq prediction with deep convolutional neural networks.☆139Updated 3 weeks ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆28Updated 3 weeks ago
- ☆33Updated last week
- Evolutionary velocity with protein language models☆90Updated last year
- Computational Optimization of DNA Activity (CODA)☆56Updated 3 weeks ago
- Species-aware DNA language modeling☆18Updated 2 years ago
- Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AI…☆34Updated 3 years ago
- The full training script for Enformer - Tensorflow Sonnet☆18Updated 3 years ago
- A repository with exploration into using transformers to predict DNA ↔ transcription factor binding☆84Updated 2 years ago
- Tokenizers and Machine Learning Models for biological sequence data☆25Updated 6 months ago
- Draw RNA secondary structures in python.☆48Updated 7 months ago
- A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.☆37Updated last year
- Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor☆48Updated 8 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆41Updated 5 months ago
- Collection of papers related to BCR repertoire analyses☆18Updated 3 years ago
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆18Updated 10 months ago
- Improving RNA structure prediction through multitask learning on diverse crowdsourced data.☆58Updated 9 months ago
- This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'☆94Updated last year
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆17Updated 9 months ago
- A python library for creating simulated regulatory DNA sequences☆38Updated 2 years ago
- Cross-protein transfer learning for variant effect prediction☆20Updated last year