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wot

wot

wot (Waddington-OT) is a tool to analyze Optimal-Transport of single-cell expression in RNA-seq data sets. The wot algorithm applies time-course data to compute the probability distributions of cells.

Topic

RNA-seq; Gene expression

Details

  • Operation: RNA-Seq analysis; RNA-seq time series data analysis
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: BSD 3-Clause "New" or "Revised" License
  • Cost: Free
  • Version name: 1.0.8
  • Maturity: Stable
  • Credit: Broad Institute, the National Institutes of Health (NIH), Helen Hay Whitney Foundation, Klarman Cell Ob-servatory at Broad Institute, Burroughs Wellcome Fund, National Science Foundation (NSF), Office of Naval Research (ONR), Chan Zuckerberg Initiative (CZI), MIT Skoltech Seed Fund.
  • Contact: Eric S. Lander lander _at_ broadinstitute.org | Aviv Regev aregev _at_ broadinstitute.org | Jian Shu jianshu _at_ broadinstitute.org
  • Collection: -

Publications

Schiebinger G, Shu J, Tabaka M, Cleary B, Subramanian V, Solomon A, Gould J, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A, Lander ES "Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming." Cell. 2019 Feb 7;176(4):928-943.e22. Jan 31. https://doi.org/10.1016/j.cell.2019.01.006
PMID: 30712874
PMCID: PMC6402800


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