CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
☆57Feb 20, 2026Updated last week
Alternatives and similar repositories for CREsted
Users that are interested in CREsted are comparing it to the libraries listed below
Sorting:
- Identifying transcription factor binding sites from neural network contribution scores☆18Nov 8, 2025Updated 3 months ago
- Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.☆19Aug 28, 2025Updated 6 months ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆79Feb 25, 2026Updated last week
- SCENIC+ analyses☆18Sep 26, 2023Updated 2 years ago
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆12Oct 16, 2025Updated 4 months ago
- Deep learning models to predict enhancers in different Drosophila embryo tissues☆20Dec 10, 2023Updated 2 years ago
- ☆13Jan 23, 2025Updated last year
- ☆21Dec 10, 2025Updated 2 months ago
- A method for analyzing scATAC-seq experiments.☆34Jun 20, 2025Updated 8 months ago
- ☆11Oct 4, 2021Updated 4 years ago
- GIANT (Gene-based data Integration and ANalysis Technique) is a method for large-scale joint analyses of atlas-level single cell data.☆14Jun 13, 2023Updated 2 years ago
- ☆27Apr 15, 2025Updated 10 months ago
- Python package to predict enhancer-gene interactions supervised on CRISPRi data☆15Nov 21, 2023Updated 2 years ago
- This repository hosts a minimal version of a Python API for BPNet.☆55Jan 24, 2026Updated last month
- Supplementary files and notebooks to recreate figures.☆21Aug 12, 2025Updated 6 months ago
- Parse ArchR arrow files to anndata h5ad☆16Dec 14, 2023Updated 2 years ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆32Jan 22, 2025Updated last year
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆72Apr 28, 2023Updated 2 years ago
- ☆20May 30, 2022Updated 3 years ago
- Computational Optimization of DNA Activity (CODA)☆67Apr 3, 2025Updated 11 months ago
- ☆65May 21, 2025Updated 9 months ago
- ☆17Updated this week
- ☆45Feb 11, 2026Updated 3 weeks ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Jan 11, 2025Updated last year
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Dec 2, 2024Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆44Jan 19, 2026Updated last month
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Feb 19, 2026Updated last week
- Annotated sequence data☆11Feb 2, 2025Updated last year
- ☆10Jan 8, 2018Updated 8 years ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆247Jan 16, 2026Updated last month
- Biological sequence analysis for the modern age.☆263Feb 22, 2026Updated last week
- Nextflow pipeline to re-process all public single-cell RNA-seq data☆31Jul 9, 2025Updated 7 months ago
- Toolset for training quantitative sequence to function models.☆23Mar 15, 2024Updated last year
- Library to extract embeddings for DNA sequences using BioFM genomics foundation model☆19Aug 13, 2025Updated 6 months ago
- ☆11Feb 6, 2023Updated 3 years ago
- Common Factor Integration & Transfer learning (cFIT) for single cell RNA-seq data☆11Jul 6, 2021Updated 4 years ago
- ☆12Nov 20, 2023Updated 2 years ago
- Camiel's scATAC-seq analysis pipeline☆13Apr 15, 2024Updated last year
- Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids☆30Aug 8, 2023Updated 2 years ago