This repository contains R source code for reproducing the VarID analysis performed in Grün D (2019) Revealing Dynamics of Gene Expression Variability in Cell State Space. Nature Methods 17(1):45-49. doi: 10.1038/s41592-019-0632-3
VarID is part of the RaceID package starting with RaceID v0.1.4 The scripts in this repository are designed for RaceID v0.1.6
Two data sets were analysed:
- mouse hematopoietic progenitors (data from Tusi, B. K. et al. Population snapshots predict early haematopoietic and erythroid hierarchies. Nature 555, 54–60 (2018))
- mouse intestinal epithelial cells (data from Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333–339 (2017))
For each of these datasets, a separate R script and input data in *.rds format are provided
Input data:
inputData_hematopoiesis.rds
Source code:
VarID_hematopoiesis.R
Input data:
inputData_intestine.rds
Source code:
VarID_intestine.R
Grün D (2019) Revealing Dynamics of Gene Expression Variability in Cell State Space. Nature Methods 17(1):45-49. doi: 10.1038/s41592-019-0632-3