URD is an R package designed for reconstructing transcriptional trajectories underlying specification or differentiation processes in the form of a branching tree, using single cell RNA-sequencing data. It is named after the Norse mythological figure who nurtures the world tree and decides all fates.

• To install, follow the instructions in INSTALL.md

• To get started, check out the Quick Start Tutorial: (View) (Download)

• The processed zebrafish embryogenesis URD object from the manuscript can be downloaded from the Broad Single-cell Portal (requires log-in).

• The full supplementary analysis from Farrell & Wang et al. is also available

Detailed changes and minor versions are listed in NEWS.md

Version 1.0 released! Our manuscript, "Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis" is online!