Our software is maintained in our Github Repository.
URD is an R package for reconstructing transcriptional trajectories underlying specification or differentiation processes in the form of a branching tree, using single cell RNA-sequencing data. URD uses a diffusion map projection of the data and works by simulating biased random walks through that projection.
URD is described and applied to early zebrafish embryogenesis in:
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.
Farrell JA & Wang Y (equal contribution), Riesenfeld SJ, Shekhar K, Regev A & Schier AF (equal contribution).
Science 26 Apr 2018. doi: 10.1126/science.aar3131