pseudogp is an R package for Bayesian inference of Gaussian Process Latent Variable models learning pseudotimes from single-cell RNA-seq. It forms a wrapper round a stan model (that requires the rstan package), as well as a set of functions to plot the posterior mean curves.
pseudogp acts on a reduced dimension representation of the data (in a similar manner to monocle and waterfall) in which it fits a probabilistic curve, allowing posterior pseudotime uncertainty to be quantified.
For a worked example see the vignette here.
# install.packages("devtools")
devtools::install_github("kieranrcampbell/pseudogp")Kieran Campbell & Christopher Yau
Wellcome Trust Centre for Human Genetics, University of Oxford