CAPITAL

Alignment of single-cell trajectory trees

Last updated: 2023-03-22

We present CAPITAL, a computational method for comparing pseudotime trajectories with tree alignment whereby trajectories including branches can be automatically compared.

Installation

• CAPITAL (ver. 1.1.2) 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.