scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).
☆29Aug 20, 2025Updated 6 months ago
Alternatives and similar repositories for scDoRI
Users that are interested in scDoRI are comparing it to the libraries listed below
Sorting:
- Code, data and analysis for moslin.☆15Oct 7, 2024Updated last year
- End-to-end analysis of spatial multi-omics data☆104Jan 26, 2026Updated last month
- Functional and Learnable Cell dynamicS☆21May 13, 2025Updated 9 months ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆26Updated this week
- ☆10Dec 4, 2023Updated 2 years ago
- Framework for Unified Single-Cell Analysis (FUSCA) is a software package for single-cell data analysis developed in R. At the moment, it …☆22Feb 14, 2023Updated 3 years ago
- ☆12Dec 23, 2025Updated 2 months ago
- ☆11May 10, 2025Updated 9 months ago
- Reproducible analyses for the NicheCompass manuscript☆13Jul 3, 2025Updated 7 months ago
- ☆12Nov 20, 2023Updated 2 years ago
- cross-species analysis of cell identities, markers and regulations☆12Jul 11, 2025Updated 7 months ago
- ☆36Nov 26, 2025Updated 3 months ago
- Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq) using AnnData h5ad files.☆12Oct 1, 2024Updated last year
- ☆13Nov 3, 2023Updated 2 years ago
- Cytograph version used for adult human-brain analysis☆97Jan 13, 2026Updated last month
- A single-cell analysis toolkit to jointly analyze samples from distinct conditions☆34Apr 2, 2025Updated 10 months ago
- ☆19Mar 31, 2023Updated 2 years ago
- R package for gene selection using k-NN graphs.☆13Jun 12, 2023Updated 2 years ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆67Jul 2, 2025Updated 7 months ago
- ☆13Aug 9, 2022Updated 3 years ago
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Jul 11, 2024Updated last year
- Sample models for the PhysiCell grammar / rules paper☆30Jul 21, 2025Updated 7 months ago
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆38Dec 17, 2025Updated 2 months ago
- ☆15Aug 17, 2023Updated 2 years ago
- ☆19Mar 31, 2024Updated last year
- DistMap☆13Nov 23, 2021Updated 4 years ago
- ☆13Sep 3, 2025Updated 5 months ago
- Trends in single cell papers☆17Sep 23, 2024Updated last year
- R package for robust clustering of single cell RNA sequencing data☆36Mar 25, 2024Updated last year
- 3D segmentation for cells and organoids of 3D multichannel images☆27Jun 24, 2025Updated 8 months ago
- ☆41Jun 24, 2025Updated 8 months ago
- Pairwise Hierarchical Model☆20Mar 11, 2022Updated 3 years ago
- Aligning gene expression trajectories of single-cell reference and query systems☆83Aug 10, 2025Updated 6 months ago
- An energy landscape-based approach for measuring developmental states and inferring cellular trajectories from single cell RNA-seq data☆18Feb 17, 2021Updated 5 years ago
- Learning cell communication from spatial graphs of cells☆113Jan 15, 2024Updated 2 years ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆118Jan 22, 2024Updated 2 years ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Jan 11, 2025Updated last year
- ☆79Jan 9, 2026Updated last month
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆79Jul 25, 2025Updated 7 months ago