Metadata-Version: 2.1
Name: spatialtis
Version: 0.3.0
Summary: spatial analysis toolkit for single-cell multiplexed tissue data
Home-page: https://github.com/Mr-Milk/SpatialTis
Author: Mr-Milk
Author-email: yb97643@um.edu.mo
License: Apache License 2.0
Description: <p align="center">
        <img src="img/Logo.svg" width="200"/>
        <p/>
        
        
        # SpatialTis
        [![Documentation Status](https://readthedocs.org/projects/spatialtis/badge/?version=latest&style=flat-square)](https://spatialtis.readthedocs.io/en/latest/?badge=latest)
        ![CI](https://flat.badgen.net/github/status/Mr-Milk/SpatialTis?icon=github&label=CI)
        ![codecov](https://flat.badgen.net/codecov/c/github/Mr-Milk/SpatialTis)
        ![pypi](https://flat.badgen.net/pypi/v/spatialtis?color=blue)
        ![licence](https://flat.badgen.net/github/license/Mr-Milk/SpatialTis)
        
        > Huge update will be happen at v0.3.0, API break, change data storage, plotting will isolate static and interactive plotting.
        
        SpatialTis is a high-performance spatial analysis toolkit for single-cell multiplexed tissue data using [`AnnData`](https://icb-anndata.readthedocs-hosted.com/en/stable/#) object as input with **parallel processing** support.
        
        **Documentation**: [![rtd](img/view_on_rtd.svg)](https://spatialtis.readthedocs.io/en/latest/)
        
        **Tutorial**: 
        - MIBI Data (Breast cancer, 180K cells) [![nbviewer](img/view_on_nbviewer.svg)](https://nbviewer.jupyter.org/github/Mr-Milk/SpatialTis-Tutorial/blob/master/Tutorial-1%20%28MIBI-dataset%29.ipynb) | [Download data](https://uofmacau-my.sharepoint.com/:u:/g/personal/yb97643_umac_mo/ET7-chqWIc9EqSEtY-foQ7IBURusGw9hlTSBC3xD_bNdgw?download=1)
        - IMC Data (Diabetes, 1.7M cells) [![nbviewer](img/view_on_nbviewer.svg)](https://nbviewer.jupyter.org/github/Mr-Milk/SpatialTis-Tutorial/blob/master/Tutorial-2%20%28IMC-dataset%29.ipynb) | [Download data](https://uofmacau-my.sharepoint.com/:u:/g/personal/yb97643_umac_mo/EXJFp1Nn_k5NphOp986lGvABmDNC_fNPGjrw5xN4NUPnRA?download=1)
        
        [Download](https://github.com/Mr-Milk/SpatialTis-Tutorial) the examples and try it on your own, see how fast SpatialTis is.
        
        ## Installation
        
        ### pypi
        
        Install the basics
        
        ```shell
        pip install spatialtis
        ```
        
        For the full features
        
        ```shell
        pip install 'spatialtis[all]'
        ```
        
        Install the current development version
        
        ```shell
        pip install git+https://github.com/Mr-Milk/SpatialTis.git
        ```
        
        ## SpatialTis modules
        
        - **Preprocessing**
        - **Data statistic**
            - Cell components
            - Cell density
            - Cell morphology
            - Cell co-occurrence
        - **Find cell neighbors**
        - **Spatial analysis**
            - Spatial distribution
            - Spatial heterogeneity
            - Hotspot detection
            - Cell-cell interaction
            - Markers co-expression
            - Spatial community detection
            - Neighbor dependent markers
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: all
