Software
Our software is maintained in our Github Repository 
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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
Data
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
In this work, we performed a single-cell RNAseq timecourse of early zebrafish embryogenesis (38,731 cells, across 12 timepoints spanning 3.3 – 12 hours post-fertilization), and reconstructed a branching specification tree leading to 25 cell types.
Browsing the data
- Browse the data interactively online 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.
- Download and install URD , 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 the data
- The processed genes x cells counts matrix (requires logging into the Broad Single-cell Portal) can be used as a starting point for your own analysis.
- Alternatively, the aligned BAM files are deposited in NCBI GEO under accession number GSE106587 along with instructions about downloading and realigning them.
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