capital 1.0.0

Single-Cell Analysis, comparing pseudotime trajectories with tree alignment

CAPITAL

Comparative pseudotime analysis of single-cell RNA-seq data

Last updated: 2021-01-12

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

Installation

• CAPITAL (ver. 1.0.0) in Python

Requirements

• Python>=3.8 (Miniconda is recommended)
• anndata>=0.7.4
• graphtools
• graphviz
• h5py<=2.10
• leidenalg
• magic-impute
• matplotlib>=3.1.2
• networkx>=2.3
• pandas>=0.21
• pydot
• scanpy>=1.6
• 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=3.8 graphviz

Next, activate the environment and pull CAPITAL from PyPI:

$ conda activate capital
$ pip install capital

Usage

Read the documentation (available very soon). 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.

Reference

Reiichi Sugihara, Yuki Kato, Tomoya Mori and Yukio Kawahara, Alignment of time-course single-cell RNA-seq data with CAPITAL, Preprint bioRxiv at https://doi.org/10.1101/859751, 2019.

Reiichi Sugihara, Yuki Kato, Tomoya Mori and Yukio Kawahara, Comparative pseudotime analysis of single-cell RNA-seq data with CAPITAL, submitted.

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If you have any questions, please contact Yuki Kato Graduate School of Medicine, Osaka University, Japan