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MetaTiME

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MetaTiME: Meta-components in Tumor immune MicroEnvironment

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# MetaTiME: Meta-components in Tumor immune MicroEnvironment 
<p align="left"><img src="https://raw.githubusercontent.com/yi-zhang/MetaTiME/main/docs/source/_static/img/logo.png" width="290" height="240"></p>

[![PyPI](https://img.shields.io/pypi/v/metatime.svg)](https://pypi.org/project/metatime/)
[![Documentation Status](https://readthedocs.org/projects/metatime/badge/?version=latest)](https://metatime.readthedocs.io/en/latest/?badge=latest)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7410180.svg)](https://doi.org/10.5281/zenodo.7410180)

MetaTiME learns data-driven, interpretable, and reproducible gene programs by integrating millions of single cells from hundreds of tumor scRNA-seq data. The idea is to learn a map of single-cell space with biologically meaningful directions from large-scale data, which helps understand functional cell states and transfers knowledge to new data analysis. MetaTiME provides pretrained meta-components (MeCs) to automatically annotate fine-grained cell states and plot signature continuum for new single-cells of tumor microenvironment.

## Installation

Create a new virtual env and activate (optional)

`python -m venv metatime-env; 
source metatime-env/bin/activate`

Use pip to install

`pip install metatime`

Installation shall be in minutes .

Next we have a tutorial on applying MetaTiME on new TME scRNAseq data to annotate cell states, scoring signature continuum, and test differential signature activity.

## Usage
### MetaTiME-Annotator
 - [Use MetaTiME to automatically annotate cell states and map signatures](https://github.com/yi-zhang/MetaTiME/blob/main/docs/notebooks/metatime_annotator.ipynb)
 - [New] MetaTiME re-training pipeline at https://github.com/yi-zhang/MetaTiMEpretrain/
 
### Interactive tutorial
[Use MetaTiME to automatically annotate cell states and map signatures ![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/yi-zhang/MetaTiME/blob/main/docs/notebooks/metatime_annotator.ipynb)

## Method 
<p align="left"><img src="https://raw.githubusercontent.com/yi-zhang/MetaTiME/main/docs/source/_static/img/fig1.png" width="700" height="400"></p>

## Reference
Repo continously being improved! More details will be updated and suggested improvements welcome.

- [Paper at Nature Communications] (https://www.nature.com/articles/s41467-023-38333-8)
- [Paper at bioRxiv](https://www.biorxiv.org/content/10.1101/2022.08.05.502989v1)

## Training Datasets

Tumor scRNAseq Data for MetaTiME @ [Zenodo](https://zenodo.org/record/7410180)

- A large collection of uniformly processed tumor single-cell RNA-seq.

- Includes raw data and MetaTiME score for the TME cells.

## Dependency

- pandas
- scanpy
- anndata
- matplotlib
- adjustText
- leidenalg
- harmonypy

Dependency version tested:
- pandas==1.1.5
- scanpy==1.8.2
- anndata==0.8.0
- matplotlib==3.5.1
- adjustText==0.7.3
- leidenalg==0.8.3

## Contact

Yi Zhang, Ph.D.

yiz [AT] ds.dfci.harvard.edu

[Twitter](https://twitter.com/Wings7Spread) |  [Website](https://yi-zhang.github.io/)
Research Fellow
Department of Data Science
Dana-Farber Cancer Institute
Harvard University T.H. Chan School of Public Health

MetaTiME

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