Citrus is a toolkit for single cell sequencing analysis under development. Citrus is written in c++ with easy-to-use R wrappers. To use Citrus, the installation of Rcpp and RcppArmadillo is required.

Now a normalized method and a clustering method are available in the distributed version.

• Method 1: scPLS: a normalization method to remove unwanted variation using both control and target genes.

  The description of methodology and algorithm can be found in the manuscript:

  Chen M, Zhou X: Normalization of single cell RNA sequencing data using both control and target genes. 2016

  which can be downloaded at: http://biorxiv.org/content/early/2016/03/21/045070.

  A vignette on how to use scPLS is distributed together with the package.

• Method 2: a clustering method which can account for confounding factors.

  The description of method and a tutorial of software on clustering will be available shortly.

Citrus relies on the following R packages: Rcpp, RcppArmadillo, genlasso, gplots. All packagess are hosted on CRAN.

install.packages ("Rcpp")
install.packages ("RcppArmadillo")
install.packages ("genlasso")
install.packages ("gplots")

Citrus can be installed from github directly as follows:

install.packages ("devtools")
library(devtools)
install_github("ChenMengjie/Citrus")

Citrus is not a short name for any of our methods. To honor Bowtie/Cufflinks and Salmon/Sailfish series, we are creating a fruit collection.

Mengjie Chen (U Chicago) Xiang Zhou (Umich)

Bug report, comments or questions please send to mengjiechen@uchicago.edu.