Software

Our software is maintained in our Github Repository.

URD

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.

Visit URD’s Github repository to get started by installing it and trying out the quick-start tutorial.

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