Single-Cell Analysis, comparing pseudotime trajectories with tree alignment
Project description
CAPITAL
Alignment of single-cell trajectory trees
Last updated: 2022-03-17
We present CAPITAL, a computational method for comparing pseudotime trajectories with tree alignment whereby trajectories including branches can be automatically compared.
Installation
- CAPITAL (ver. 1.1.0) in Python
Requirements
- Python>=3.8 (Miniconda is recommended)
- anndata>=0.7.4
- graphtools
- graphviz
- h5py>=2.10
- leidenalg
- magic-impute
- matplotlib==3.5.2
- networkx<=2.8.3
- pandas>=0.21
- pydot
- scanpy==1.9.1
- scikit-learn
- scipy>=1.4
- scprep
- tslearn
Install on Linux, Windows (WSL) and macOS
Create a new environment for CAPITAL (recommended):
conda create -n capital python=3.9 graphviz
Next, activate the environment and pull CAPITAL from PyPI:
conda activate capital
pip install capital
Usage
Read the documentation. CAPITAL uses a single-cell analysis toolkit Scanpy in its implementation so that one can also use Scanpy's useful functions including preprocessing, plotting and datasets in the CAPITAL environment.
Code Ocean
We also provide a Code Ocean compute capsule to reproduce our results.
Reference
Reiichi Sugihara, Yuki Kato, Tomoya Mori and Yukio Kawahara, Alignment of single-cell trajectory trees with CAPITAL, Nature Communications, vol. 13, 5972, 2022. [Link]
If you have any questions, please contact Yuki Kato. Graduate School of Medicine, Osaka University, Japan.
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