pinellolab / EPInformer
code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
☆34Updated 2 months ago
Alternatives and similar repositories for EPInformer:
Users that are interested in EPInformer are comparing it to the libraries listed below
- ☆17Updated 5 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆24Updated 3 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆46Updated this week
- Computational Optimization of DNA Activity (CODA)☆53Updated 2 weeks ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆31Updated last week
- single cell foundation model for Gene network inference and more☆42Updated this week
- Dataloader for applying sequence models to personalized genomics☆22Updated this week
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆30Updated this week
- Tools for sgRNA calling in direct capture Perturb-seq data☆31Updated last year
- Molecular interactions inference from single-cell multi-omics data☆22Updated 2 months ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆68Updated 6 months ago
- Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).☆19Updated 2 months ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆60Updated 9 months ago
- Evaluating genomic sequence models for explaining personalized expression variation☆19Updated last year
- ☆25Updated last month
- CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets☆49Updated 3 months ago
- This repository hosts a minimal version of a Python API for BPNet.☆35Updated 3 weeks ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆17Updated 2 weeks ago
- ☆26Updated this week
- ☆49Updated 2 months ago
- ☆19Updated last year
- Gene regulatory network inference for RNA velocity and pseudotime data☆22Updated 11 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆65Updated 6 months ago
- Single cell omics biology annotations☆48Updated this week
- Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets☆36Updated 9 months ago
- ☆25Updated last week
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆36Updated 2 weeks ago
- Toolset for training quantitative sequence to function models.☆21Updated 10 months ago
- Code for scKINETICS (ISMB 2023)☆21Updated last year
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆27Updated 3 months ago