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| Open AccessEvaluating batch correction methods for image-based cell profiling
Batch effects can limit the usefulness of image-based profiling data. Here, authors benchmark ten popular batch correction techniques on a large Cell Painting dataset, evaluating multiple metrics. They identify Harmony and Seurat RPCA as top methods across diverse complex scenarios.
- John Arevalo
- , Ellen Su
- & Shantanu Singh
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Article
| Open AccessData fusion and multivariate analysis for food authenticity analysis
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
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Article
| Open AccessComparative analysis of dimension reduction methods for cytometry by time-of-flight data
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
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Article
| Open AccessDeep learning-enabled segmentation of ambiguous bioimages with deepflash2
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
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Article
| Open AccessComprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data
Quality control (QC) is a crucial step in single-cell RNA-seq data analysis. Here, the authors present the SCTK-QC pipeline which generates and visualizes a comprehensive set of QC metrics to streamline the process of detecting and removing poor quality cells and other artifacts.
- Rui Hong
- , Yusuke Koga
- & Joshua D. Campbell
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Article
| Open AccessQuantifying and comparing radiation damage in the Protein Data Bank
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
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Article
| Open AccessSMAP is a pipeline for sample matching in proteogenomics
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
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Article
| Open AccessImproved analyses of GWAS summary statistics by reducing data heterogeneity and errors
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
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Article
| Open AccessSpearheading future omics analyses using dyngen, a multi-modal simulator of single cells
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
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Article
| Open AccessA practical solution to pseudoreplication bias in single-cell studies
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
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Article
| Open AccessHarmonization of quality metrics and power calculation in multi-omic studies
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
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Article
| Open AccessDetection and removal of barcode swapping in single-cell RNA-seq data
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