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Installation
Getting started
Preparations
Download of datasets
Extract images of individual samples from whole slide image
Step-by-step analysis walkthrough
Automated image registration
Data preprocessing and analysis
Working with histological annotations and regions
Cropping the data
Cell type annotation
Investigate gene expression and cell density along an axis
Multi-sample analysis
Introduction to the
InSituExperiment
class
Differential gene expression and GO term enrichment analysis
Data import
Build an
InSituData
object from custom data
Addition of data segmented with proseg
Plotting
Spatial plotting functionalities
Plot colorlegends for publication
Analysis from manuscript
Differential gene expression analysis for publication Figure 4
API
Repository
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