MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

By Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L. King, Luis B. Agellon, Jianguo Xia. Nucleic Acids Res., 2017

1,612 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4b636e983c20e6909326acf7fbde928cd47625df

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Citations in the corpus

MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data (2023, positive): “Version 1.0 of MicrobiomeAn-alyst was de v eloped to provide a user-friendly w e b-based platf orm f or bench r esear chers to perform compr ehensi v e exploratory analysis on common abundance profiles and taxonomic signatures ( 11 ).”
Current challenges and best-practice protocols for microbiome analysis (2019, methodology): “Two widely used tools for statistical downstream analysis on microbial data are Calypso [169] and MicrobiomeAnalyst [170].”
Role of the microbiome in human development (2019, background): “Efforts to standardise specimen preparation 108 and analytical protocols and to increase the availability of the growing body of data 109–111 are increasing.”