Genentech / regLMLinks
Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
☆46Updated 11 months ago
Alternatives and similar repositories for regLM
Users that are interested in regLM are comparing it to the libraries listed below
Sorting:
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆35Updated 5 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆73Updated last week
- Computational Optimization of DNA Activity (CODA)☆61Updated 5 months ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆41Updated 2 months ago
- ☆41Updated last month
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆22Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆44Updated 10 months ago
- ☆18Updated last year
- For fine-tuning Enformer using paired WGS & gene expression data☆22Updated 3 weeks ago
- ☆32Updated 7 months ago
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆23Updated last year
- The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)☆36Updated 2 years ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆19Updated last week
- Machine learning methods for DNA sequence analysis.☆54Updated 3 weeks ago
- ☆78Updated 2 years ago
- deep learning-inspired explainable sequence model for transcription initiation☆97Updated 6 months ago
- ☆80Updated 3 weeks ago
- Knowledge-primed neural networks☆38Updated 2 years ago
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆92Updated last month
- Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.☆27Updated last month
- a framework for predicting global protein-protein interaction networks from dynamic mass spec data☆24Updated last year
- ☆76Updated 2 months ago
- ☆13Updated 3 weeks ago
- Dataloader for applying sequence models to personalized genomics☆27Updated this week
- Evaluating genomic sequence models for explaining personalized expression variation☆19Updated last year
- surrogate quantitative interpretability for deepnets☆24Updated last month
- ☆72Updated last year
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆46Updated this week
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆66Updated 3 years ago
- Modeling complex perturbations with CellFlow☆85Updated this week