p-koo / evoaugLinks
Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics
☆24Updated 6 months ago
Alternatives and similar repositories for evoaug
Users that are interested in evoaug are comparing it to the libraries listed below
Sorting:
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆24Updated last year
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆32Updated 11 months ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆38Updated 8 months ago
- BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow☆39Updated last year
- ☆18Updated last year
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Updated last year
- Jax code for functional genomics ML☆14Updated 9 months ago
- Code for paper "Principled feature attribution for unsupervised gene expression analysis"☆12Updated 2 years ago
- Interpretable splicing model☆21Updated 2 years ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆43Updated 5 months ago
- A python library for creating simulated regulatory DNA sequences☆39Updated 2 years ago
- Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements☆23Updated 9 months ago
- Elucidating the Utility of Genomic Elements with Neural Nets☆70Updated last year
- a framework for predicting global protein-protein interaction networks from dynamic mass spec data☆24Updated last year
- ☆19Updated last week
- Predicting gene expression levels from genomic sequences☆55Updated 5 years ago
- Machine learning methods for DNA sequence analysis.☆57Updated 3 months ago
- Deep learning models to predict enhancers in different Drosophila embryo tissues☆20Updated 2 years ago
- Efficient algorithms for designing orthogonal DNA sequence libraries☆13Updated last year
- Knowledge-primed neural networks☆38Updated 2 years ago
- Annotated sequence data☆11Updated 10 months ago
- a light structured Residual autoencoder and mutual nearest neighbor Paring guided Adversarial Network for scRNA-seq batch correction☆15Updated 2 years ago
- Standard set of data-loaders for training and making predictions for DNA sequence-based models.☆82Updated last year
- A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input ge…☆20Updated last week
- Nextflow pipeline to re-process all public single-cell RNA-seq data☆30Updated 5 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆71Updated 2 years ago
- ☆33Updated 3 years ago
- Genomic sequence preprocessing toolkit☆13Updated last month
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆43Updated 2 months ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆21Updated 3 months ago