SpatialCells

SpatialCells is an open-source software package designed to perform region-based exploratory analysis and characterization of tumor microenvironments using multiplexed single-cell data. The package uses the Anndata framework and complements existing single-cell analysis packages such as MCMICRO and SCIMAP. In particular, SpatialCells can efficiently analyze samples comprising millions of cells without manual annotation and automatically extract quantitative features of cell regions, enabling subsequent association analyses and machine learning predictions at scale.

Contents:

• Quick Start Guide
  • Installation
• Tutorials
  • 0: Basic Functions
  • 1: Spatial and Measurement Functions
  • 2: Tumor Proliferation Analysis
  • 3: Immune Infiltration Overlap Analysis
  • 4: Macro and Micro Regions Analysis
  • 5: Loading and Saving Regions
  • 6: Visium Data Analysis
  • 7: Working with Squidpy
  • 8: Working with SCIMAP and Scanpy
• Functions Reference
  • spatialcells.preprocessing
  • spatialcells.spatial
  • spatialcells.measurements
  • spatialcells.plotting
  • spatialcells.utils

• Index