MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data.
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TLDR
This work introduces MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies.Abstract:
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation. Here, we introduce MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies. MicrobiomeAnalyst contains four modules - the Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction based on 16S rRNA marker gene data; the Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics or metatranscriptomics data; the Taxon Set Enrichment Analysis module helps interpret taxonomic signatures via enrichment analysis against >300 taxon sets manually curated from literature and public databases; finally, the Projection with Public Data module allows users to visually explore their data with a public reference data for pattern discovery and biological insights. MicrobiomeAnalyst is freely available at http://www.microbiomeanalyst.ca.read more
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Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.
TL;DR: This protocol details MicrobiomeAnalyst, a user-friendly, web-based platform for comprehensive statistical, functional, and meta-analysis of microbiome data, a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces.
Evaluación de la diversidad taxonómica y funcional de la comunidad microbiana relacionada con el ciclo del nitrógeno en suelos de cultivo de arroz con diferentes manejos del tamo
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TL;DR: The impact of the quema de arroz on the microorganismos edaficos in the disponibilidad and ciclaje de nutrientes is poco conocido, es por esto que el retorno de los residuos vegetales al suelo ha been propuesto como una alternativa de manejo eficiente de los residentes pos-cosecha.
Journal ArticleDOI
MicroRNAs and complex diseases: from experimental results to computational models.
TL;DR: Twenty state-of-the-art computational models of predicting miRNA-disease associations from different perspectives are reviewed, including five feasible and important research schemas, and future directions for further development of computational models are summarized.
Journal ArticleDOI
Culturing the human microbiota and culturomics
Jean-Christophe Lagier,Grégory Dubourg,Matthieu Million,Frédéric Cadoret,Melhem Bilen,Florence Fenollar,Anthony Levasseur,Jean-Marc Rolain,Pierre-Edouard Fournier,Didier Raoult +9 more
TL;DR: How culturomics has extended the understanding of bacterial diversity, and how it can be applied to the study of the human microbiota and the potential implications for human health are described.
Journal ArticleDOI
Role of the microbiome in human development.
TL;DR: The role of the microbiome in human development, including evolutionary considerations, and the maternal/fetal relationships, contributions to nutrition and growth are reviewed.
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