> For the complete documentation index, see [llms.txt](https://help.multiomics.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.multiomics.illumina.com/icm/reference/list-of-analysis-tasks-by-data-type/spatial-transcriptomics.md). # Spatial Transcriptomics ## Expression Count Matrix Examples of expression count matrix are Spatial - Cells, Single cell counts, Filtered counts, Normalized counts. Analysis tasks that can be invoked from expression count matrix are listed below. | Task Menu Section | Analysis Task Name | | ------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Report | | | Annotation/Metadata | | | QA/QC | | | Pre-analysis tools | | | Filtering | | | Normalization and scaling | | | Batch removal | | | Statistics | | | Exploratory analysis | | | Trajectory analysis | | | Biological interpretation | | | Classification | | | Conversion | | ## PCA Analysis tasks that can be invoked from PCA data node are listed below. | Task Menu Section | Analysis Task Name | | -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Annotation/Metadata | | | Batch removal | | | Statistics | | | Exploratory analysis | | | Conversion | | ## Differential Analysis Result Analysis tasks that can be invoked from differential analysis result (e.g., ANOVA, Wilcoxon) are listed below. | Task Menu Section | Analysis Task Name | | ------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | QA/QC | | | Filtering | | | Statistics | | | Exploratory analysis | | | Motif detection | | | Biological interpretation | | --- # Agent Instructions This documentation is published with GitBook. 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