Summary: Recently, an increasing number of methodological approaches have been proposed to tackle the complexity of metagenomics and microbiome data. In this scenario, reproducibility and replicability have become two critical issues, and the development of computational frameworks for the comparative evaluations of such methods is of utmost importance. Here, we present benchdamic, a Bioconductor package to benchmark methods for the identification of differentially abundant taxa.
Availability And Implementation: benchdamic is available as an open-source R package through the Bioconductor project at https://bioconductor.org/packages/benchdamic/.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825737 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btac778 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Wearable technology in inflammatory bowel disease: current state and future direction.
Expert Rev Med Devices
January 2025
Division of Gastroenterology, P.D Hinduja Hospital, Mumbai, India.
Introduction: Wearables are electronic devices worn on the body to collect health data. These devices, like smartwatches and patches, use sensors to gather information on various health parameters. This review highlights current use and the potential benefit of wearable technology in patients with inflammatory bowel disease (IBD).
View Article and Find Full Text PDFData-Driven Approach for Designing Eco-Friendly Heterocyclic Compounds for the Soil Microbiome.
Environ Sci Technol
January 2025
College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. of China.
Soil microbiota plays crucial roles in maintaining the health, productivity, and nutrient cycling of terrestrial ecosystems. The persistence and prevalence of heterocyclic compounds in soil pose significant risks to soil health. However, understanding the links between heterocyclic compounds and microbial responses remains challenging due to the complexity of microbial communities and their various chemical structures.
View Article and Find Full Text PDFLong-Term Impact of Childhood Dental Attendance on Perceived Adult Oral Health: The British Cohort Study.
J Public Health Dent
January 2025
Dental Public Health, Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK.
Objective: To evaluate the effect of childhood dental attendance pattern on self-rated oral health in middle adulthood among the British population.
Methods: Data from the 1970 British Cohort Study involving participants born in England, Scotland, and Wales were used. Self-rated oral health was assessed at age 46.
HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.
Database (Oxford)
January 2025
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues.
View Article and Find Full Text PDFA scoping review evaluating the current state of gut microbiota and its metabolites in valvular heart disease physiopathology.
Eur J Clin Invest
January 2025
Department of Cardiology, Bern University Hospital, Inselspital, Bern, Switzerland.
Background: The human microbiome is crucial in regulating intestinal and systemic functions. While its role in cardiovascular disease is better understood, the link between intestinal microbiota and valvular heart diseases (VHD) remains largely unexplored.
Methods: Peer-reviewed studies on human, animal or cell models analysing gut microbiota profiles published up to April 2024 were included.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!