gagneurlab / scoobyView external linksLinks
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
☆54Nov 1, 2025Updated 3 months ago
Alternatives and similar repositories for scooby
Users that are interested in scooby are comparing it to the libraries listed below
Sorting:
- Analyses related to the Borzoi paper.☆25Dec 14, 2025Updated 2 months ago
- ☆11Oct 10, 2024Updated last year
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆94Nov 13, 2025Updated 3 months ago
- ☆11Feb 6, 2023Updated 3 years ago
- Species-aware DNA language models capture regulatory elements and their evolution☆27Aug 21, 2023Updated 2 years ago
- This repository hosts a minimal version of a Python API for BPNet.☆55Jan 24, 2026Updated 3 weeks ago
- ☆19Jan 24, 2025Updated last year
- Toolbox of the Human Neural Organoid Cell Atlas☆29Feb 2, 2026Updated last week
- A method for analyzing scATAC-seq experiments.☆34Jun 20, 2025Updated 7 months ago
- Parse ArchR arrow files to anndata h5ad☆16Dec 14, 2023Updated 2 years ago
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆12Oct 16, 2025Updated 3 months ago
- Multiome GRN inference.☆135Apr 19, 2024Updated last year
- A python port of the R package SCTransform:☆21Jul 10, 2021Updated 4 years ago
- Identifying transcription factor binding sites from neural network contribution scores☆17Nov 8, 2025Updated 3 months ago
- ☆11Sep 7, 2023Updated 2 years ago
- Annotated sequence data☆11Feb 2, 2025Updated last year
- ☆13Jan 23, 2025Updated last year
- ENNGene: an Easy Neural Network model building tool for Genomics☆11Mar 31, 2022Updated 3 years ago
- ☆11Nov 12, 2025Updated 3 months ago
- ☆25Aug 20, 2024Updated last year
- Toolset for training quantitative sequence to function models.☆23Mar 15, 2024Updated last year
- code to run sei and obtain sei and sequence class predictions☆111Dec 20, 2022Updated 3 years ago
- ☆11Oct 4, 2021Updated 4 years ago
- ☆11Jul 18, 2025Updated 6 months ago
- ☆10Dec 11, 2024Updated last year
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆39Mar 27, 2025Updated 10 months ago
- GraphPart, a data partitioning method for ML on biological sequences☆33Oct 26, 2023Updated 2 years ago
- Standard set of data-loaders for training and making predictions for DNA sequence-based models.☆83Sep 3, 2024Updated last year
- ☆58Jan 23, 2026Updated 3 weeks ago
- Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…☆15Jun 25, 2025Updated 7 months ago
- Jax code for functional genomics ML☆14Mar 5, 2025Updated 11 months ago
- SuperCell for Cytometry data☆13Oct 14, 2025Updated 4 months ago
- Iso-Seq reads simulator for PacBio and ONT full-length isoform sequencing technologies☆16Mar 1, 2022Updated 3 years ago
- Reproducing the experiments in the paper☆11Dec 14, 2021Updated 4 years ago
- Lineage Tracing by Integrating Mutation and Transcriptomic data☆13Jun 16, 2020Updated 5 years ago
- A Matlab package to perform Pareto Task Inference (ParTI), which infers tasks from high-dimensional datasets.☆15Jan 21, 2020Updated 6 years ago
- R package IReNA☆30Nov 13, 2024Updated last year
- A python package for chromVAR☆33May 1, 2023Updated 2 years ago