Metadata-Version: 2.1
Name: capital
Version: 1.0.8
Summary: Single-Cell Analysis, comparing pseudotime trajectories                 with tree alignment
Home-page: https://github.com/ykat0/capital
Author: Reiichi Sugihara, Yuki Kato, Tomoya Mori, Yukio Kawahara
Author-email: reiichi.sugihara@gmail.com
License: BSD-3-Clause
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: BSD License
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Description-Content-Type: text/markdown
Requires-Dist: anndata (>=0.7.4)
Requires-Dist: graphtools
Requires-Dist: graphviz
Requires-Dist: h5py (>=2.10.0)
Requires-Dist: leidenalg
Requires-Dist: magic-impute
Requires-Dist: matplotlib (>=3.1.2)
Requires-Dist: networkx (==2.8.3)
Requires-Dist: numpy (>=1.17.0)
Requires-Dist: pandas (>=0.21)
Requires-Dist: pydot
Requires-Dist: scanpy (==1.9.1)
Requires-Dist: scikit-learn
Requires-Dist: scipy (>=1.4)
Requires-Dist: scprep
Requires-Dist: tslearn

[![PyPI version](https://badge.fury.io/py/capital.svg)](https://badge.fury.io/py/capital)
[![Documentation Status](https://readthedocs.org/projects/capital/badge/?version=latest)](https://capital.readthedocs.io/en/latest/?badge=latest)

# CAPITAL

## Alignment of single-cell trajectory trees

Last updated: 2022-06-28

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

## Installation
* CAPITAL (ver. 1.0.8) in Python

### Requirements
* Python>=3.8 ([Miniconda](https://docs.conda.io/en/latest/miniconda.html) is recommended)
* anndata>=0.7.4
* graphtools
* graphviz
* h5py>=2.10
* leidenalg
* magic-impute
* matplotlib>=3.1.2
* 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](https://capital.readthedocs.io/en/latest/). CAPITAL uses a single-cell analysis toolkit [Scanpy](https://scanpy.readthedocs.io/en/latest/index.html) in its implementation so that one can also use Scanpy's useful functions including preprocessing, plotting and datasets in the CAPITAL environment.

