Metadata-Version: 2.3
Name: cytocraft
Version: 0.0.6
Summary: The Cytocraft package provides prediction of chromosome conformation based on spatial transcriptomic.
Project-URL: Homepage, https://github.com/YifeiSheng/Cytocraft
Project-URL: Issues, https://github.com/YifeiSheng/Cytocraft/issues
Project-URL: Repository, https://github.com/YifeiSheng/Cytocraft.git
Author-email: Yifei Sheng <yfsheng6@gmail.com>, Shiying Li <shiyingli7-c@my.cityu.edu.hk>, Shuai Cheng Li <sc.li@cityu.edu.hk>
License: MIT license
License-File: LICENSE
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Requires-Dist: scanpy
Requires-Dist: shapely
Description-Content-Type: text/markdown

# Cytocraft

<p align="center">
	<img src=https://github.com/YifeiSheng/Cytocraft/raw/main/figure/Figure1.Overview.png>
</p>

## Overview

The Cytocraft package provides prediction of chromosome conformation based on spatial transcriptomic.

## Installaion

```
pip install cytocraft
```

## Quick Start

### Run Cytocraft

This example shows the usage of Cytocraft.

	python craft.py ./data/SS200000108BR_A3A4_scgem.Spinal_cord_neuron.csv ./results/ Mouse

## Usage
```
python craft.py [-h] [-p PERCENT] [-c CELLTYPE] [--ctkey CTKEY] [--cikey CIKEY] [--seed SEED] gem_path out_path {Human,Mouse,Axolotls,Monkey}
```
### positional arguments:

  gem_path              `Path to gem file`

  out_path              `Output path to save results`

  {Human,Mouse,Axolotls,Monkey} `Species of the input data`

### optional arguments:

  -h, --help     `show this help message and exit`

  -p, --percent  `percent of gene for rotation derivation, default: 0.001`

  -t, --threshold  `The maximum proportion of np.nans allowed in a column(gene) in W, default: 0.90`

  -c, --celltype `Path of file containing cell types`

  --ctkey `Key of celltype column in the cell type file`

  --cikey `Key of cell id column in the cell type file`

  --seed  `Random seed`
