Metadata-Version: 2.4
Name: scmiracle
Version: 0.1.0
Summary: MIRACLE: continual integration and label transfer for single-cell multimodal data.
Author-email: labomics <omicshub@outlook.com>
License: MIT
Project-URL: Homepage, https://github.com/sc-miracle/miracle
Project-URL: Issues, https://github.com/sc-miracle/miracle/issues
Keywords: single-cell,multi-omics,integration,pytorch,scanpy,anndata,mudata,continual learning,continual integration
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
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# MIRACLE: A Continue Learning Framework for Scalable Multimodal Integration

## Tutorials & API

<p align="left">
<a href="https://miracle-docs.readthedocs.io/en/latest/" target="_blank" style="font-size: 20px;">Documentation</a>
</p>

## Reproducibility

<p align="left">
<a href="https://github.com/sc-miracle/miracle-reproducibility" target="_blank" style="font-size: 20px;">sc-miracle/miracle-reproducibility</a>
</p>


## Installation

To set up your environment, please follow these steps:

```bash
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](https://satijalab.org/seurat/) | Specifically for sketch sampling techniques |
| Signac  | v1.6.0                               |                                     |

---

## Data

The following datasets are available for download:

| Data         | URL  | Description| Notes |
| ------------ | -------- | -------- | -------- |
| DOTEA          | [📥](https://pub-cfde59ed245349228f47377c9ae32dd3.r2.dev/miracle/DOTEA.zip) |RNA+ADT+ATAC, 8 batches|Used in tutorial 1 |
| PBMC Atlas   | [📥](https://pub-cfde59ed245349228f47377c9ae32dd3.r2.dev/miracle/pbmc_atlas.zip) |RNA+ADT+ATAC, 33 batches| Used in tutorial 2|
| Bone Marrow  | [📥](https://pub-cfde59ed245349228f47377c9ae32dd3.r2.dev/miracle/bone_marrow.zip) |RNA+ADT+ATAC, 1 batch|Used in tutorial 2|
