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README.md

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 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.

scCancer-workflow

(Click to view larger workflow picture)

System Requirements

  • 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")

Hint:

  1. A dependent package NNLM was removed from the CRAN repository recently, so an error about it may be reported during the installation. If so, you can install its a formerly available version by following codes or install manually from its archive.
install.packages("RcppArmadillo")
install.packages("RcppProgress")
install.packages('http://lifeome.net/software/sccancer/packages/NNLM_0.4.3.tar.gz', type='source')
  1. Some dependent packages on GitHub (as follows) may not be able to install automatically, if you encounter such errors, please refer to their GitHub and install them via corresponding commands.
  • SoupX: devtools::install_github("constantAmateur/SoupX")
  • harmony: devtools::install_github("immunogenomics/harmony")
  • liger: devtools::install_github("MacoskoLab/liger")

Usage

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

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

For multi-datasets, following is a generated HTML report for three kidney cancer samples integration analysis:

Citation

Please use the following citation:

Wenbo Guo, Dongfang Wang, Shicheng Wang, Yiran Shan, Jin Gu. 2019. bioRxiv doi: https://doi.org/10.1101/800490

License

GPL-3

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A package for automated processing of single cell RNA-seq data in cancer

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