Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA seq. Such experiments require specialized tools for primary processing such as GRAND-SLAM, and specialized tools for downstream analyses. grandR provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data.
grandR is available from CRAN. Install grandR using the following commands on the R console:
install.packages("grandR")
library(Seurat)You can also install the development version from github:
require("devtools")
devtools::install_github("erhard-lab/grandR")
library(grandR)First have a look at the Getting started vignette.
Then, go through the Differential expression or the Kinetic modeling vignette, which provide a comprehensive walk-through of the two main settings of nucleotide conversion experiments.
There are also additional vignettes: