MIRACLE: continual integration and label transfer for single-cell multimodal data.
Project description
MIRACLE: A Continue Learning Framework for Scalable Multimodal Integration
Tutorials & API
Reproducibility
sc-miracle/miracle-reproducibility
Installation
To set up your environment, please follow these steps:
conda create -n miracle python=3.11.11
conda activate miracle
pip install -r requirements.txt
Python Package Dependencies:
| Package | Version |
|---|---|
| Python | v3.11.11 |
| PyTorch | v2.1.2 |
| scikit-learn | v1.3.2 |
| Scanpy | v1.9.6 |
| scib | v1.1.4 |
R Package Dependencies:
| Package | Version | Notes |
|---|---|---|
| Seurat | v4.1.0 | For general data preprocessing and analysis |
| Seurat | v5.2.1 | Specifically for sketch sampling techniques |
| Signac | v1.6.0 |
Data
The following datasets are available for download:
| Data | URL | Description | Notes |
|---|---|---|---|
| DOTEA | 📥 | RNA+ADT+ATAC, 8 batches | Used in tutorial 1 |
| PBMC Atlas | 📥 | RNA+ADT+ATAC, 33 batches | Used in tutorial 2 |
| Bone Marrow | 📥 | RNA+ADT+ATAC, 1 batch | Used in tutorial 2 |
Release history Release notifications | RSS feed
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