1. Introduction

The scCancer package focuses on processing and analyzing droplet-based scRNA-seq data for cancer research. Except basic data processing steps, this package takes several special considerations for cancer-specific features.

The workflow of scCancer mainly consists of three modules: scStatistics, scAnnotation, and scCombination.

• The scStatistics performs basic statistical analyses of raw data and quality control.
• The scAnnotation performs functional data analyses and visualizations, such as low dimensional representation, clustering, cell type classification, cell malignancy estimation, cellular phenotype analyses, gene signature analyses, cell-cell interaction analyses, etc.
• The scCombination perform multiple samples data integration, batch effect correction and analyses visualization.

After the computational analyses, detailed and graphical reports were generated in user-friendly HTML format.

(Click to view larger workflow picture)