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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: >= 16G (for a data with ~10000 cells)
• R version: >= 3.4.0

Installation

Please install or update the package devtools by running install.packages("devtools") firstly.

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.

We also provide a kidney cancer example data, and here are the generated reports: report-scStat.html, report-scAnno.html.

Citation

Please use the following citation:

License

GPL-3 © G-Lab, Tsinghua University