Introduction

Single-cell gene expression data provide invaluable resources for systematic characterization of cellular hierarchy in multi-cellular organisms. However, cell lineage reconstruction is still often associated with significant uncertainty due to technological constraints. Such uncertainties have not been taken into account in current methods. We present ECLAIR (Ensemble Cell Lineage Analysis with Improved Robustness), a novel computational method for the statistical inference of cell lineage relationships from single-cell gene expression data. ECLAIR uses an ensemble approach to improve the robustness of lineage predictions, and provides a quantitative estimate of the uncertainty of lineage branchings. We show that the application of ECLAIR to published datasets successfully reconstructs known lineage relationships and significantly improves the robustness of predictions. ECLAIR is a powerful bioinformatics tool for single-cell data analysis. It can be used for robust lineage reconstruction with quantitative estimate of prediction accuracy.

Publications

  1. Robust lineage reconstruction from high-dimensional single-cell data.
    Cite this
    Giecold G, Marco E, Garcia SP, Trippa L, Yuan GC, 2016-08-01 - Nucleic acids research

Credits

  1. Gregory Giecold
    Developer

    Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, United States of America

  2. Eugenio Marco
    Developer

    Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, United States of America

  3. Sara P Garcia
    Developer

    Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, United States of America

  4. Lorenzo Trippa
    Developer

    Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, United States of America

  5. Guo-Cheng Yuan
    Investigator

    Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, United States of America

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Summary
AccessionBT006182
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByGuo-Cheng Yuan