Preprocessing Strategy Registry for Single-Cell Workflows

An environment that maps single-letter codes to standardized Seurat preprocessing operations. Each entry is a function of the form function(...) that wraps a core Seurat step (e.g., normalization, PCA, clustering)

This registry enables compact, composable pipeline definitions (e.g., via character strings like "onvps" for "Create → Normalize → VariableFeatures → Scale → PCA") and supports both standard (NormalizeData) and SCTransform-based workflows.

Usage

SCPreProcessStrategy

Format

An object of class environment of length 11.

Available Operations

o

Create Seurat object from count matrix (SeuratObject::CreateSeuratObject)

n

Normalize data (Seurat::NormalizeData)

v

Find variable features (Seurat::FindVariableFeatures)

s

Scale data (Seurat::ScaleData)

p

Run PCA (Seurat::RunPCA)

c

Find clusters (Seurat::FindClusters)

e

Find neighbors (Seurat::FindNeighbors)

t

Run t-SNE (Seurat::RunTSNE)

u

Run UMAP (Seurat::RunUMAP)

r

SCTransform (Seurat::SCTransform)

i

Integrate layers (Seurat::IntegrateLayers)

Usage Notes

• These functions are not intended for direct interactive use. They are internal building blocks for workflow engines (i.e., SCPreProcess).

• You can access any operation via SCPreProcessStrategy$letter, but doing so bypasses pipeline validation and error handling.

• To add more operations, use RegisterSeuratMethod()

See also

Other single_cell_preprocess: FilterTumorCell(), FindRobustElbow(), Pattern2Colname(), QCPatternDetect(), RegisterSeuratMethod(), SCAnnotate(), SCIntegrate(), SCPreProcess(), compatible_with_3.0.2()