pinellolab / EPInformerLinks
code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
☆44Updated 8 months ago
Alternatives and similar repositories for EPInformer
Users that are interested in EPInformer are comparing it to the libraries listed below
Sorting:
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆68Updated last month
- Computational Optimization of DNA Activity (CODA)☆60Updated 4 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆42Updated last week
- ☆23Updated 11 months ago
- This repository hosts a minimal version of a Python API for BPNet.☆47Updated 3 weeks ago
- deep learning-inspired explainable sequence model for transcription initiation☆97Updated 5 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆83Updated last month
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆77Updated last year
- ☆23Updated last year
- ☆34Updated 2 months ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆86Updated 10 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆29Updated last week
- code to run sei and obtain sei and sequence class predictions☆106Updated 2 years ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 4 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…☆43Updated last week
- ☆36Updated last week
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆89Updated 5 months ago
- For fine-tuning Enformer using paired WGS & gene expression data☆19Updated 2 months ago
- ☆31Updated 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
- Evaluating genomic sequence models for explaining personalized expression variation☆20Updated last year
- Toolset for training quantitative sequence to function models.☆23Updated last year
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆97Updated 6 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 6 months ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆175Updated 3 weeks ago
- A modular framework for multimodal cross-cell-type transcriptional regulation models☆84Updated last week
- TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…☆25Updated 2 years ago
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated 8 months ago
- Machine learning methods for DNA sequence analysis.☆51Updated 3 weeks ago
- single cell foundation model for Gene network inference and more☆96Updated this week