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.
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To install, follow the instructions in INSTALL.md
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To get started, check out the Quick Start Tutorial: (View) (Download)
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The processed zebrafish embryogenesis URD object from the manuscript can be downloaded from the Broad Single-cell Portal (requires log-in).
Version 1.0 released! Our manuscript, "Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis" is online!