Orchestrating Spatial Omics Data
1
Preface
1.1
Software information and conventions
2
Introduction
2.1
Why reading this book?
2.2
Bioconductor
3
Spatially-resolved transcriptomics
3.1
Preprocessing Steps
3.2
Image segmetation
3.3
Loupe Browser
3.4
Space Ranger
4
Spatially-resolved omics
4.1
Preprocessing Steps
4.2
Image segmetation
5
Analysis
5.1
Quality control
5.2
Normalization
5.3
Feature selection
5.4
Dimensionality reduction
5.5
Clustering
5.6
Marker genes
5.7
Spot-level deconvolution
6
Final Words
References
Published with bookdown
Orchestrating Spatially-Resolved MultiOmics Analysis with Bioconductor
Chapter 5
Analysis
Some
significant
applications are demonstrated in this chapter.
5.1
Quality control
5.2
Normalization
5.3
Feature selection
5.4
Dimensionality reduction
5.5
Clustering
5.6
Marker genes
5.7
Spot-level deconvolution