Danko-Lab / clipnetLinks
A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution
☆12Updated last month
Alternatives and similar repositories for clipnet
Users that are interested in clipnet are comparing it to the libraries listed below
Sorting:
- Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.☆15Updated last month
- ☆17Updated 9 months ago
- deep learning-inspired explainable sequence model for transcription initiation☆96Updated 4 months ago
- For fine-tuning Enformer using paired WGS & gene expression data☆19Updated 2 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 6 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆64Updated 2 years ago
- ☆64Updated last month
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆43Updated 8 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆68Updated 3 weeks ago
- This repository hosts a minimal version of a Python API for BPNet.☆47Updated last week
- Dataloader for applying sequence models to personalized genomics☆26Updated last week
- ☆31Updated 5 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…☆42Updated last month
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆80Updated last month
- Computational Optimization of DNA Activity (CODA)☆60Updated 3 months ago
- ☆35Updated last week
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆77Updated last year
- ☆23Updated last year
- code to run sei and obtain sei and sequence class predictions☆106Updated 2 years ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆42Updated this week
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 3 months ago
- ☆23Updated 11 months ago
- Compute generation probabilities of CDR3 amino acid and nucleotide sequences☆53Updated 3 years ago
- Analyses related to the Borzoi paper.☆13Updated last month
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆70Updated 2 weeks ago
- Evaluating genomic sequence models for explaining personalized expression variation☆20Updated last year
- ☆40Updated 4 years ago
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated 8 months ago
- ☆18Updated last year
- ☆19Updated 3 months ago