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Article
| Open Accessrworkflows: automating reproducible practices for the R community
Reproducibility is essential for the progress of research, yet achieving it remains elusive even in computational fields. Here, authors develop the rworkflows suite, making robust CI/CD workflows easy and freely accessible to all R package developers.
- Brian M. Schilder
- , Alan E. Murphy
- & Nathan G. Skene
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| Open AccessAdvancing reuse of genetic parts: progress and remaining challenges
Issues with data reuse have been recognized in synthetic biology and the broader scientific community. Policies and standards fall short as machine reasoning is not emphasised and enforcement is lacking. We discuss the progress, remaining challenges, and possible solutions.
- Jeanet Mante
- & Chris J. Myers
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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 AccessInteroperable slide microscopy viewer and annotation tool for imaging data science and computational pathology
There is a lack of standardisation in slide microscopy imaging data. Here the authors report Slim, an open-source, web-based slide microscopy viewer implementing the Digital Imaging and Communications in Medicine (DICOM) standard to achieve interoperability with a range of existing medical imaging systems.
- Chris Gorman
- , Davide Punzo
- & Markus D. Herrmann
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Article
| Open AccessLibrary adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing
Adding library adaptors to DNA samples is an essential step in preparing samples for next-generation sequencing. Here, Gunter et al. describe the development of Control Library Adaptors (CAPTORs), that correct sequencing errors and normalise quantitative biases in Nanopore libraries.
- Helen M. Gunter
- , Scott E. Youlten
- & Tim R. Mercer
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| Open AccessA framework to efficiently describe and share reproducible DNA materials and construction protocols
DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Here the authors introduce QUEEN, a framework to describe and share DNA materials and construction protocols.
- Hideto Mori
- & Nozomu Yachie
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| Open AccessBenchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases
Here, the authors use simulated quantitative gut microbial communities to benchmark the performance of 13 common data transformations in determining diversity as well as microbe-microbe and microbe-metadata associations, finding that quantitative approaches incorporating microbial load variation outperform computational strategies in downstream analyses, urging for a widespread adoption of quantitative approaches, or recommending specific computational transformations whenever determination of microbial load of samples is not feasible.
- Verónica Lloréns-Rico
- , Sara Vieira-Silva
- & Jeroen Raes
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Article
| Open AccessA diploid assembly-based benchmark for variants in the major histocompatibility complex
Accurate, phased assemblies are a key tool in understanding the human genome, particularly in highly polymorphic regions like the medically important MHC. Here the authors provide an assembly-based benchmark for this difficult-to-characterize region.
- Chen-Shan Chin
- , Justin Wagner
- & Justin M. Zook
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Article
| Open AccessA universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
Standard units of measurement are required for a quantitative description of the genome. Here, the authors present a universal synthetic DNA ladder that can measure genetic abundance in next-generation sequencing libraries.
- Andre L. M. Reis
- , Ira W. Deveson
- & Tim R. Mercer
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Article
| Open AccessSynthetic microbe communities provide internal reference standards for metagenome sequencing and analysis
Complex microbial communities pose a challenge to metagenomic analysis. Here the authors develop ‘sequins’, internal DNA standards that represent a synthetic community of artificial genomes.
- Simon A. Hardwick
- , Wendy Y. Chen
- & Tim R. Mercer