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

AnnData-based multi-sample analysis workflows

Many analysis tools (e.g. batch correction, niche analysis, etc.) are based on the AnnData format. This notebook demonstrates how data of an InSituExperiment object can be converted into an AnnData, processed using such tools and how the information can be imported back into an InSituExperiment.

Tutorial: Exporting and Importing AnnData with InSituExperiment