gagneurlab / scoobyLinks
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
☆48Updated last month
Alternatives and similar repositories for scooby
Users that are interested in scooby are comparing it to the libraries listed below
Sorting:
- This repository hosts a minimal version of a Python API for BPNet.☆53Updated last month
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆42Updated 2 months ago
- A method for analyzing scATAC-seq experiments.☆34Updated 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…☆52Updated last week
- ☆25Updated last year
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆32Updated 10 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆88Updated 3 weeks ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆86Updated 2 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 8 months ago
- A python package for chromVAR☆31Updated 2 years ago
- High-definition modeling of chromatin + transcriptomics data☆25Updated 7 months ago
- Toolset for training quantitative sequence to function models.☆23Updated last year
- ☆26Updated 6 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆54Updated last week
- Tools for sgRNA calling in direct capture Perturb-seq data☆39Updated 2 years ago
- Analyses related to the Borzoi paper.☆23Updated 2 months ago
- Dataloader for applying sequence models to personalized genomics☆27Updated last week
- Benchmark of GRNs using the GRETA pipeline☆29Updated last week
- Pipeline to run scE2G☆31Updated last month
- Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.☆17Updated 3 months ago
- Learning motif contributions to cell transitions using sequence features and graphs.☆28Updated last year
- Snakemake workflow for comparing E-G links to experimental data☆23Updated last month
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆71Updated 2 years ago
- Molecular interactions inference from single-cell multi-omics data☆28Updated last month
- TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…☆25Updated 3 years ago
- Machine learning methods for DNA sequence analysis.☆57Updated 3 months ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆21Updated 2 months ago
- ☆24Updated 2 months ago
- Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.☆50Updated 10 months ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Updated last month