Genentech / polygraph
Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of regulatory elements.
☆28Updated 3 weeks ago
Alternatives and similar repositories for polygraph:
Users that are interested in polygraph are comparing it to the libraries listed below
- Computational Optimization of DNA Activity (CODA)☆56Updated 2 weeks ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆46Updated last week
- ☆33Updated this week
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆18Updated 9 months ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆38Updated 6 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 2 months ago
- ☆18Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆41Updated 4 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆61Updated last year
- For fine-tuning Enformer using paired WGS & gene expression data☆14Updated last week
- Dataloader for applying sequence models to personalized genomics☆24Updated last week
- ☆21Updated last year
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆28Updated last week
- ExplaiNN: interpretable and transparent neural networks for genomics☆47Updated 2 weeks ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆18Updated 2 weeks ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆26Updated 2 years ago
- ☆27Updated 2 months ago
- Knowledge-primed neural networks☆36Updated 2 years ago
- Genomic sequence preprocessing toolkit☆12Updated last month
- Toolset for training quantitative sequence to function models.☆23Updated last year
- ☆25Updated 3 months ago
- code to run sei and obtain sei and sequence class predictions☆102Updated 2 years ago
- ☆17Updated 5 months ago
- Evaluating genomic sequence models for explaining personalized expression variation☆19Updated last year
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆35Updated 5 months ago
- surrogate quantitative interpretability for deepnets☆21Updated 3 weeks ago
- Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…☆14Updated 4 months ago
- a framework for predicting global protein-protein interaction networks from dynamic mass spec data☆24Updated last year
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆32Updated last week
- Gene regulatory network inference for RNA velocity and pseudotime data☆25Updated 3 weeks ago