VAMPS: a website for visualization and analysis of microbial population structures. The MG-RAST metagenomics database and portal in 2015. MetaboAnalystR 2.0: from raw spectra to biological insights. MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. Microbiome datasets are compositional: and this is not optional. Metagenomic microbial community profiling using unique clade-specific marker genes. Kraken: ultrafast metagenomic sequence classification using exact alignments. One Codex: a sensitive and accurate data platform for genomic microbial identification. DADA2: high-resolution sample inference from Illumina amplicon data. UPARSE: highly accurate OTU sequences from microbial amplicon reads.
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Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Current understanding of the human microbiome. The vocabulary of microbiome research: a proposal. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. The Human Microbiome Project: a community resource for the healthy human microbiome. The Earth Microbiome project: successes and aspirations.
The complete protocol can be executed in ~70 min. In summary, MicrobiomeAnalyst offers a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces. The last two sections will describe the key steps involved in using the PPD and TSEA modules for meta-analysis and visual exploration of the results.
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We will then demonstrate how to perform predictive functional profiling and introduce several unique features of the SDP module for functional analysis. This protocol will first introduce the MDP module by providing a step-wise description of how to prepare, process and normalize data perform community profiling identify important features and conduct correlation and classification analysis. MicrobiomeAnalyst currently contains four modules: Marker-gene Data Profiling (MDP), Shotgun Data Profiling (SDP), Projection with Public Data (PPD), and Taxon Set Enrichment Analysis (TSEA). It enables researchers and clinicians with little or no bioinformatics training to explore a wide variety of well-established methods for microbiome data processing, statistical analysis, functional profiling and comparison with public datasets or known microbial signatures.
MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of common data outputs generated from current microbiome studies.
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