Quality control articles within Nature Communications

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  • Article
    | Open Access

    Using two different mass spectrometric platforms, authors demonstrate how metabolomic data fusion and multivariate analysis can be used to accurately identify the geographic origin and production method of salmon.

    • Yunhe Hong
    • , Nicholas Birse
    •  & Christopher T. Elliott

  • Article
    | Open Access

    Dimension reduction (DR) is a key step of Cytometry by Time-of-Flight (CyTOF) data analysis. Here, the authors benchmark 21 DR methods on 110 real and 425 synthetic CyTOF samples, finding a high level of complementarity between the methods, and providing a comprehensive set of user guidelines.

    • Kaiwen Wang
    • , Yuqiu Yang
    •  & Tao Wang

  • Article
    | Open Access

    The signal-to-noise ratio in bioimages is often low, which is problematic for segmentation. Here the authors report a deep learning method, deepflash2, to facilitate the segmentation of ambiguous bioimages through multi-expert annotations and integrated quality assurance.

    • Matthias Griebel
    • , Dennis Segebarth
    •  & Christoph M. Flath

  • Article
    | Open Access

    Radiation damage hampers protein structure determination by X-ray crystallography. Here, the AUs introduce the Bnet metric, a single value summarising the extent of radiation damage of a protein crystal structure, and use Bnet to detect radiation damage in structures deposited in the Protein Data Bank.

    • Kathryn L. Shelley
    •  & Elspeth F. Garman

  • Article
    | Open Access

    Sample mix-up is a potential problem in large-scale omic studies due to the complexity of sample processing. Here, the authors present a pipeline for sample matching in proteogenomics to verify sample identity and ensure data integrity.

    • Ling Li
    • , Mingming Niu
    •  & Xusheng Wang

  • Article
    | Open Access

    Analyses of summary statistics from GWAS are subject to biases due to errors in the discovery GWAS or linkage disequilibrium reference data set or heterogeneity between data sets. Here, the authors propose a quality control method to be added to analysis of GWAS summary data that can reduce such biases.

    • Wenhan Chen
    • , Yang Wu
    •  & Jian Yang

  • 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

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