geng-lee / varid_analysis

VarID analysis of murine hematopoietic progenitors and intestinal epithelial cells. VarID is part of RaceID v0.1.4

VarID analysis

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:

1. mouse hematopoietic progenitors (data from Tusi, B. K. et al. Population snapshots predict early haematopoietic and erythroid hierarchies. Nature 555, 54–60 (2018))
2. 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

Hematopoietic progenitors

Input data:

inputData_hematopoiesis.rds

Source code:

VarID_hematopoiesis.R

Intestinal epithelial cells

Input data:

inputData_intestine.rds

Source code:

VarID_intestine.R

Reference:

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