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	Spatial report
Annotation/Metadata	Annotate cells Annotate features Annotate Visium image Publish attributes to study Attribute report
QA/QC	Feature distribution Single cell QA/QC Cell barcode QA/QC
Pre-analysis tools	Hashtag demultiplexing (Available on normalized data only) Pseudobulk Split by feature type Generate group cell counts Merge matrices
Filtering	Filter features Filter cells Split by attribute Downsample cells
Normalization and scaling	Normalization Normalization to baseline Scran deconvolution TF-IDF normalization Scale expression (Available on normalized data only) Impute missing values SCTransform
Batch removal	General linear model Seurat3 integration (Available on normalized data only)
Statistics	Differential analysis Correlation Descriptive statistics Compute biomarkers Cox Regression Kaplan-Meier Spatially Variable Genes (Available on non-normalized data only)
Exploratory analysis	Graph-based clustering K-means clustering Compare clusters PCA t-SNE UMAP Hierarchical clustering / heatmap AUCell SVD BANSKY - Spatial Domain Identification (Available on non-normalized data only) CellPhoneDB (Available on normalized data only)
Trajectory analysis	Monocle 2 Monocle 3
Biological interpretation	GSEA Gene set ANOVA Gene set enrichment
Classification	Classify cell type ScType cell classification (Available on non-normalized data only) Train classifier
Conversion	Export to h5ad files Export matrix

PCA

Analysis tasks that can be invoked from PCA data node are listed below.

Task Menu Section	Analysis Task Name
Annotation/Metadata	Publish attributes to study
Batch removal	General linear model Harmony
Statistics	Differential analysis Correlation Descriptive statistics Compute biomarkers Cox Regression Kaplan-Meier
Exploratory analysis	Graph-based clustering K-means clustering Compare clusters t-SNE UMAP Find multimodal neighbors SVD
Conversion	Export matrix

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	Feature distribution
Filtering	Differential analysis filter
Statistics	Descriptive statistics
Exploratory analysis	Hierarchical clustering / heatmap Merge differential expression results
Motif detection	Detect de novo motifs Search for known motifs
Biological interpretation	Gene set enrichment Correlation Engine atlases Correlation Engine pathways