Multi-sample analysis

This set of tutorials introduces the analysis of multiple samples using InSituPy’s InSituExperiment class.

Introduction to the InSituExperiment class

Notebook introducing the concepts behind the InSituExperiment class to analyze multiple samples.

Introduction to the InSituExperiment class

Split datasets per sample

Sometimes data from multiple samples can be present in one dataset. This notebook shows how to extract the data from each individual sample.

Split datasets

Generate pseudobulk data

Notebook showing how to generate pseudobulk data from an InSituExperiment class.

Pseudobulk Differential Gene Expression Analysis in InSituPy

Extract individual images from a merged dataset

Notebook showing how to extract individual images from merged multi-sample data.

Extract images of individual samples from whole slide image

Anndata workflow for multi-sample analysis

Notebook introducing a multi-sample analysis workflow based on AnnData objects.

Tutorial: Exporting and Importing AnnData with InSituExperiment

Import workflow based on the Vannan et al. paper

Notebook demonstrating multi-sample data from Vannan et al. paper.

Demonstrate reading of data from Vannan et al.