Imaging-based platforms
21
Sub-cellular analysis
OSTA
Welcome
Introduction
1
Introduction
2
Spatial omics
3
Interoperability
4
Infrastructure
5
Importing data
6
Datasets
Sequencing-based platforms
7
Introduction
8
Quality control
9
Processing
10
Deconvolution
11
Workflow: Visium DLPFC
12
Workflow: Visium CRC
13
Workflow: Visium HD
14
Workflow: spatialLIBD
Imaging-based platforms
15
Introduction
16
Segmentation
17
Quality control
18
Processing
19
Neighborhood analysis
20
Cell communication
21
Sub-cellular analysis
22
Workflow: Xenium
23
Workflow: CosMx
Technology-agnostic/cross-platform/downstream analyses
24
Introduction
25
Dimension reduction
26
Clustering
27
Spatially variable genes
28
Gene/feature-set signatures
29
Spatial statistics
30
Registration
31
Multiple-sample differential expression
32
Workflow: Xenium + Visium
Appendices
A
Acknowledgments
B
Related resources
C
Session information
Table of contents
References
Imaging-based platforms
21
Sub-cellular analysis
21
Sub-cellular analysis
r BiocStyle::Githubpkg("SydneyBioX/SpatialFeatures")
References
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20
Cell communication
22
Workflow: Xenium