spatialtis 0.2.0

spatial analysis toolkit for single-cell multiplexed tissue data

SpatialTis

SpatialTis is a high-performance spatial analysis toolkit for single-cell multiplexed tissue data using AnnData object as input with parallel processing support.

Documentation:

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]

# In some terminal environment you may try
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
  • Marker influence by neighbor cell/marker