metatime 1.2.2

Beta MetaTiME: annotate TME scRNA cell states

MetaTiME: Meta-components in Tumor immune MicroEnvironment

MetaTiME is a framework to generate data-driven, interpretable, and reproducible gene programs by integrating millions of single cells from hundreds of tumor scRNA-seq data. Applied on large-scale tumor scRNA data with 1.7 million Tcells, MetaTiME thus utilize the meta-components to automatically annotate cell states for single-cells from tumor microenvironment. ( * BETA version, Currently under development :)

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 .

Interactive tutorials

MetaTiME-Annotator

Use MetaTiME to automatically annotate cell states and map signatures

Method

Usage

• Use MetaTiME to automatically annotate cell states and map signatures

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

Reference

Manuscript In Revision. Repo continously being improved! More details will be updated.

Paper at bioRxiv

[Journal Article doi pending]

Training Datasets

Tumor scRNAseq Data for MetaTiME @ Zenodo

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

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

Contact

Yi Zhang, Ph.D.

yiz [AT] ds.dfci.harvard.edu

Twitter | Website

Research Fellow

Department of Data Science

Dana-Farber Cancer Institute

Harvard University T.H. Chan School of Public Health