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 2 months ago
Alternatives and similar repositories for polygraph:
Users that are interested in polygraph are comparing it to the libraries listed below
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆38Updated 4 months ago
- Computational Optimization of DNA Activity (CODA)☆56Updated 2 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆42Updated 2 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 2 months ago
- Dataloader for applying sequence models to personalized genomics☆22Updated this week
- ☆32Updated this week
- ☆21Updated last year
- ☆18Updated last year
- Toolset for training quantitative sequence to function models.☆23Updated last year
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆37Updated 5 months ago
- ☆17Updated 5 months ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆28Updated 3 weeks ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆26Updated 2 years ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆58Updated last year
- ExplaiNN: interpretable and transparent neural networks for genomics☆47Updated last month
- Evaluating genomic sequence models for explaining personalized expression variation☆19Updated last year
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆24Updated this week
- For fine-tuning Enformer using paired WGS & gene expression data☆12Updated last week
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆17Updated last week
- Gene regulatory network inference for RNA velocity and pseudotime data☆25Updated this week
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆17Updated 8 months ago
- High-definition modeling of chromatin + transcriptomics data☆22Updated this week
- ☆19Updated 7 months ago
- ☆27Updated last month
- code to run sei and obtain sei and sequence class predictions☆99Updated 2 years ago
- Knowledge-primed neural networks☆35Updated 2 years ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆72Updated 8 months ago
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆32Updated this week
- Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…☆12Updated 4 months ago
- ☆57Updated 6 months ago