Quality control

  • Article
    | Open Access

    To benchmark single cell bioinformatics tools, data simulators can provide a robust ground truth. Here the authors present dyngen, a multi-modal simulator, and apply it to aligning cell developmental trajectories, cell-specific regulatory network inference and estimation of RNA velocity.

    • Robrecht Cannoodt
    • , Wouter Saelens
    •  & Yvan Saeys
  • Article
    | Open Access

    Single cell genomics uses cells from the same individual, or pseudoreplicates, that can introduce biases and inflate type I error rates. Here the authors apply generalized linear mixed models with a random effect for individual, to properly account for both zero inflation and the correlation structure among cells within an individual.

    • Kip D. Zimmerman
    • , Mark A. Espeland
    •  & Carl D. Langefeld
  • Article
    | Open Access

    Multi-omics studies are popular but lack rigorous criteria for experimental design. We define Figures of Merit across omics to comparatively describe their performance, and present new algorithms for sample size calculation in multi-omics experiments aiming either at feature selection or sample classification.

    • Sonia Tarazona
    • , Leandro Balzano-Nogueira
    •  & Ana Conesa
  • Article
    | Open Access

    DNA barcode swapping results in mislabelling of sequencing reads between multiplexed samples. Here, the authors investigate the severity and consequences of barcode swapping for single-cell RNA-seq data, and develop a computational method to exclude swapped reads.

    • Jonathan A. Griffiths
    • , Arianne C. Richard
    •  & John C. Marioni