shirondru / enformer_fine_tuningLinks
For fine-tuning Enformer using paired WGS & gene expression data
☆15Updated 3 weeks ago
Alternatives and similar repositories for enformer_fine_tuning
Users that are interested in enformer_fine_tuning are comparing it to the libraries listed below
Sorting:
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆43Updated 6 months ago
- Toolset for training quantitative sequence to function models.☆23Updated last year
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 4 months ago
- Evaluating genomic sequence models for explaining personalized expression variation☆20Updated last year
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆56Updated last week
- ☆22Updated last year
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated 6 months ago
- Dataloader for applying sequence models to personalized genomics☆26Updated this week
- ☆34Updated last month
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆31Updated 2 months ago
- ☆17Updated 7 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆38Updated 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
- ☆23Updated 9 months ago
- ☆25Updated this week
- ☆18Updated last year
- Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…☆14Updated 6 months ago
- Computational Optimization of DNA Activity (CODA)☆59Updated 2 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…☆39Updated last week
- Code for reproducing the Sei manuscript results☆17Updated 3 years ago
- ☆28Updated 4 months ago
- Saluki, a method to predict mRNA half-lives from sequence☆24Updated 2 years ago
- PyTorch implementation of Basenji2.☆15Updated last month
- Snakemake workflow for comparing E-G links to experimental data☆18Updated this week
- High-definition modeling of chromatin + transcriptomics data☆24Updated last month
- A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution☆12Updated 3 weeks ago
- ☆13Updated 4 months ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆19Updated 2 months ago
- ☆16Updated last month
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆26Updated 2 years ago