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scCancer

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 two parts: scStatistics and scAnnotation.

• The scStatistics performs basic statistical analysis of raw data and quality control.
• The scAnnotation performs functional data analyses and visualizations, such as low dimensional representation, clustering, cell type classification, malignancy estimation, cellular phenotype scoring, gene signature analysis, etc.

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

System Requirements

• Memery: >= 32G (for a data with ~10000 cells)
• R version: >= 3.5.0

Installation

Firstly, please install or update the package devtools by running

install.packages("devtools")

Then the scCancer can be installed via

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

Usage

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

We also provide an example data of kidney cancer from 10X Genomics, and here are the generated reports:

• report-scStat.html
• report-scAnno.html

Citation

Please use the following citation:

License

GPL-3