xu-lab/SINCERA

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

SINCERA

An R S4 implementation of the SINCERA pipeline for single-cell RNA-seq profiling analysis

Developed by Minzhe Guo

Installation

• In R or RStudio, type the following command to install devtools

  install.packages("devtools")
  library(devtools)
  

• Then, use devtools to install SINCERA from github

  devtools::install_github("xu-lab/SINCERA")
  

• Use library() to activate SINCERA

  library(SINCERA)
  

Demonstration

• A demonstration of using SINCERA to analysis E16.5 mouse lung single cell data can be found at https://github.com/minzheguo/SINCERA/blob/master/demo/mouselung.e16.5.R.

• A demonstration of using SINCERA to analysis Human IPF and normal epithelial single cell data can be found at https://github.com/minzheguo/SINCERA/blob/master/demo/humanIPF.R.

Citation

• Guo M, Wang H, Potter S, Whitsett JA, Xu Y. 2015. SINCERA: A Computational Pipeline for Single Cell RNA-seq Profiling Analysis. PLoS Computational Biology. 11:11, e1004575.