jmschrei / ledidiLinks
Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
☆87Updated 2 months ago
Alternatives and similar repositories for ledidi
Users that are interested in ledidi are comparing it to the libraries listed below
Sorting:
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆39Updated last month
- Jax code for functional genomics ML☆14Updated 5 months ago
- Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors☆40Updated last year
- Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…☆76Updated 2 weeks ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆46Updated 10 months ago
- Diverse Genomic Embedding Benchmark☆46Updated 5 months ago
- Benchmarking DNA Language Models on Biologically Meaningful Tasks☆122Updated 9 months ago
- Draw RNA secondary structures in python.☆48Updated 2 months ago
- Tokenizers and Machine Learning Models for biological sequence data☆25Updated 11 months ago
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆67Updated 2 years ago
- A repository with exploration into using transformers to predict DNA ↔ transcription factor binding☆85Updated 3 years ago
- This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'☆95Updated 2 years ago
- Standard set of data-loaders for training and making predictions for DNA sequence-based models.☆81Updated 11 months ago
- ☆39Updated last month
- A python library for creating simulated regulatory DNA sequences☆38Updated 2 years ago
- Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics☆23Updated 2 months ago
- Interpretable splicing model☆20Updated 2 years ago
- Interpretable genotype-phenotype landscape modeling☆35Updated last year
- Species-aware DNA language modeling☆18Updated 2 years ago
- Interpretation by Deep Generative Masking for Biological Sequences☆37Updated 3 years ago
- Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.☆17Updated 3 years ago
- Machine learning methods for DNA sequence analysis.☆53Updated last month
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆35Updated 5 months ago
- Biological Network Integration using Convolutions☆62Updated last year
- Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor☆48Updated last year
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆19Updated last week
- Modeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.☆50Updated 6 years ago
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆22Updated last year
- Comprehensive Python client for the Uniprot REST API☆51Updated 2 months ago
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆20Updated last year