PseudotimeDE is a robust method that accounts for the uncertainty in pseudotime inference and thus identifies DE genes along cell pseudotime with well-calibrated p-values. PseudotimeDE is flexible in allowing users to specify the pseudotime inference method and to choose the appropriate model for scRNA-seq data.
PseudotimeDE is developed to perfrom the differential expression (DE) test on genes along pseudotime (trajectory). Users can choose the pseudotime inference methods based on their preference. Basically, PseudotimeDE will use subsampling to capture the uncertainty of inferred pseudotime, and generate well-calibrated p-values.
The package is not on Bioconductor or CRAN yet. For installation please use the following codes in R.
install.packages("devtools")
library(devtools)
devtools::install_github("SONGDONGYUAN1994/PseudotimeDE")Please note that PseudotimeDE can be computationally intensive; we recommend users to allocate at least 10 cores unless they want to ignore the uncertainty of inferred pseudotime.
For usage, please check the vignettes. If you meet problems, please contact dongyuansong@ucla.edu.