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Standard Seurat Analysis Pipeline for Spatial Transcriptomics

Source: R/Preprocessing.R
Seurat_pipeline.Rd

Performs a complete Seurat analysis pipeline for spatial transcriptomics data, including normalization, feature selection, scaling, PCA, clustering, and UMAP/t-SNE dimensionality reduction. Also generates spatial feature plots.

Usage

Seurat_pipeline(
  seurat_obj = NULL,
  data_type = "stRNA",
  resolution_index = seq(0.1, 1.3, 0.2),
  runTSNE_index = FALSE,
  assay_nm = NULL
)

Arguments

seurat_obj

A Seurat object containing spatial transcriptomics data

data_type

Character, data type - "stRNA" (spatial) or "scRNA" (single-cell) (default: "stRNA")

resolution_index

Numeric vector, clustering resolutions to test (default: seq(0.1, 1.3, 0.2))

runTSNE_index

Logical, whether to perform t-SNE (default: FALSE)

assay_nm

Character, assay name (default: NULL, auto-detected)

Value

A Seurat object with processed data and cluster annotations

Examples

if (FALSE) { # \dontrun{
# Run standard pipeline on spatial data
stRNA <- Seurat_pipeline(
  seurat_obj = stRNA,
  resolution_index = seq(0.2, 1.0, 0.2)
)
} # }