spatial analysis toolkit for single-cell multiplexed tissue data
Project description
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
object as input with parallel processing support.
Tutorial:
- MIBI Data (Breast cancer, 180K cells) | Download data
- IMC Data (Diabetes, 1.7M cells) | Download data
Download the examples and try it on your own, see how fast SpatialTis is.
Installation
pypi
Install the basics
pip install spatialtis
For the full features
pip install 'spatialtis[all]'
Install the current development version
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
Project details
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