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URD
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URD

URD is a tool to reconstruct transcriptional trajectories in single-cell RNA-seq (scRNA-seq) data. The URD algorithm computes a branching tree.



URD

URD is a tool to reconstruct transcriptional trajectories in single-cell RNA-seq (scRNA-seq) data. The URD algorithm computes a branching tree.

Topic

Gene expression; RNA-seq

Details

  • Operation: RNA-Seq analysis; Prediction and recognition
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v3
    • Cost: Free
  • Version name: 1.1.0
  • Credit: NIH, the Allen Discovery Center for Cell Lineage Tracing, Jane Coffin Childs Memorial Fund, Charles A. King Trust, Howard Hughes Medical Institute, the Klarman Cell Observatory.
  • Contact: ALEX SCHIER schier _at_ fas.harvard.edu
  • Collection: -

Publications

Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF "Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis." Science. 2018 Jun 1;360(6392). https://doi.org/10.1126/science.aar3131
PMID: 29700225
PMCID: PMC6247916


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