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.


URD is described and applied to early zebrafish embryogenesis in:

Farrell JA*, Wang Y*, Riesenfeld SJ, Shekhar K, Regev A*, Schier AF*. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 26 Apr 2018. doi: 10.1126/science.aar3131

Browsing the Data

The zebrafish embryogenesis data (38,731 cells, 12 developmental time points from 3.3–12 hours post fertilization) can be browsed in two forms:

  1. Easiest/Quickest: Browse the data in the Broad Single-cell Portal ( This allows plotting the expression of genes of interest on the 3D force-directed layout, tSNE projection, or spatially assigned 50% epiboly cells.
  2. Best: Download and install URD (see "Getting URD" below), then download the zebrafish data as a pre-processed URD object (requires logging into the Broad Single-cell Portal). This allows more responsive plotting on the 3D force-directed layout, the dendrogram layout, or the tSNE projections (including dual-color plotting of multiple genes), as well as isolation of particular cell populations, differential expression, and more.

Getting URD

URD is an R package hosted in Github ( Detailed installation instructions are located in the repository.

Getting the data

If you want to do your own analysis with our data, you can obtain it in two forms:

  1. The processed counts matrix can be downloaded and used as a starting point for your own analysis:  ( — requires logging into the Broad Single-cell Portal).
  2. BAM files are deposited in NCBI GEO under accession number GSE106587.

Contact Us

For questions regarding URD, please email Jeff Farrell (, Yiqun Wang (, or Alexander Schier (