pinellolab / EPInformer
code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
☆31Updated 2 weeks ago
Related projects ⓘ
Alternatives and complementary repositories for EPInformer
- Computational Optimization of DNA Activity (CODA)☆39Updated 2 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆19Updated last month
- ☆14Updated 3 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆58Updated 4 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆43Updated last year
- ☆22Updated 7 months ago
- ☆15Updated last month
- Evaluating genomic sequence models for explaining personalized expression variation☆16Updated 11 months ago
- ☆27Updated this week
- ☆16Updated 2 weeks ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆66Updated 4 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆54Updated last year
- Pipeline for efficient genomic data processing.☆20Updated 2 months ago
- ☆17Updated last year
- single cell foundation model for Gene network inference and more☆24Updated this week
- Toolset for training quantitative sequence to function models.☆20Updated 8 months ago
- TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…☆23Updated 2 years ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆17Updated this week
- RNA-seq prediction with deep convolutional neural networks.☆89Updated 3 weeks ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆60Updated 6 months ago
- Molecular interactions inference from single-cell multi-omics data☆22Updated 2 weeks ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆79Updated last month
- Gene regulatory network inference for RNA velocity and pseudotime data☆22Updated 9 months ago
- ☆45Updated 2 months ago
- Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).☆18Updated 3 weeks ago
- ☆16Updated 8 months ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆26Updated last month
- This repository hosts a minimal version of a Python API for BPNet.☆32Updated 3 months ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆49Updated this week
- ☆26Updated last year