CAPITAL

Alignment of single-cell trajectory trees

Last updated: 2022-03-22

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

Installation

CAPITAL (ver. 1.1.1) 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.

Metadata

Release files for capital 1.1.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for capital 1.1.2
File	Size	Uploaded
capital-1.1.2.tar.gz	25.7 kB	Mar 21, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for capital 1.1.2
File	Interpreter	ABI	Platform	Reset
capital-1.1.2-py3-none-any.whl 27.8 kB Mar 21, 2023	Python 3	none	any	Details

Total release size: 53.5 kB

Release files / capital-1.1.2.tar.gz

Download URL	capital-1.1.2.tar.gz
Size	25.7 kB
Tags	Source
SHA-256 checksum How to use checksums	`9de121640db30b0004a031d801f300ee3a2e51ff8d0d45d9b1a59e9f6123bbc6`
BLAKE2b-256 checksum How to use checksums	`00735f9e98c8127d01470cd98c195be6efc1080d733beef59ec7478454db6183`
Upload date	Mar 21, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.10.9`

Release files / capital-1.1.2-py3-none-any.whl

Download URL	capital-1.1.2-py3-none-any.whl
Size	27.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`38b615ad2042e47fbef0f95f5203a83b8c24ef8fe84b053d28eb3f29eabedbf1`
BLAKE2b-256 checksum How to use checksums	`9394e544f530e30e1b51cf92905e91cc1e32a8560929162382d81feb3aceec5d`
Upload date	Mar 21, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.10.9`