p-koo / evoaugLinks
Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics
☆21Updated last year
Alternatives and similar repositories for evoaug
Users that are interested in evoaug are comparing it to the libraries listed below
Sorting:
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 4 months ago
- Jax code for functional genomics ML☆13Updated 3 months ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆39Updated 8 months ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆31Updated 2 months ago
- ☆18Updated last year
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆19Updated 11 months ago
- a framework for predicting global protein-protein interaction networks from dynamic mass spec data☆24Updated last year
- ☆34Updated last month
- Computational Optimization of DNA Activity (CODA)☆59Updated 2 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆43Updated 6 months ago
- Annotated sequence data☆11Updated 4 months ago
- Create cell sentences from sequencing data☆22Updated 9 months ago
- ☆25Updated last month
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆56Updated 2 weeks ago
- For fine-tuning Enformer using paired WGS & gene expression data☆15Updated 3 weeks ago
- Interpretable splicing model☆20Updated last year
- Genomic sequence preprocessing toolkit☆12Updated last week
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆63Updated 2 years ago
- Knowledge-primed neural networks☆37Updated 2 years ago
- Evaluating genomic sequence models for explaining personalized expression variation☆20Updated last year
- ☆64Updated 9 months ago
- ☆22Updated last year
- BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow☆34Updated 9 months ago
- surrogate quantitative interpretability for deepnets☆21Updated 2 months ago
- Interpretation by Deep Generative Masking for Biological Sequences☆37Updated 3 years ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆36Updated last month
- A command-line tool to mitigate homology-based data leakage in sequence-to-expression models☆14Updated 2 months ago
- ☆58Updated 8 months ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆19Updated 2 months ago
- Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.☆25Updated 2 months ago