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scCancer

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

The scCancer pipeline consists of two parts: scStatistics and scAnnotation.

• The scStatistics implements quality control for cells and genes.
• The scAnnotation implements normal analysis and annotate the cells' low-dimension coordinates, cluster, cell type, cell cycle, malignancy, gene set signatures, expression program, and so on.

After these analyses, user-friendly graphic reports will be generated.

Installation

The scCancer package can be installed via

library(devtools)
devtools::install_github("wguo-research/scCancer")

Usage

The vignette of scCancer can be found in the project wiki.

Citation

Please use the following citation: