scFlowKit

scFlowKit is a modular and extensible toolkit written in R for streamlined single-cell RNA-seq analysis.

Designed to support both standard pipelines and customizable workflows, it allows bioinformatics researchers to rapidly process, integrate, and visualize scRNA-seq data.

🔧 Key Features

• Compatible with both Seurat and SingleCellExperiment objects
• Includes powerful general-purpose function read_sce() to read .h5, .mtx, .loom, and .h5ad formats
• Integrated modules for:
  • Quality control
  • Batch correction
  • Dimensionality reduction
  • Clustering & annotation
  • Visualization
• Structured annotation and CLI prompts for usability

📦 Use Cases

• Rapid startup for scRNA-seq project prototyping
• Teaching material for reproducible single-cell workflows
• Integration with other downstream analysis frameworks

scFlowKit is actively maintained and aims to bridge the gap between flexible scripting and reproducible workflows in single-cell transcriptomics.