ArticleBMC bioinformatics2020
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Dietary and water probiotics enhance immunity, modulate microbiota, and increase survival of Penaeus vannamei challenged with V. parahaemolyticus.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Bioinformatic tools for microbiome analysis: from raw sequences to biological insights.Frontiers in microbiology · 2026Review
- BiombalanceAntioxidants (Basel, Switzerland) · 2025Article
- Investigating the effects of synbiotics, postbiotics and bacilli in the modulation of gut microbiota and the survival of Litopenaeus vannamei challenged with Vibrio parahaemolyticus.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Underground guardians: how collagen and chitin amendments shape soil microbiome structure and function for Meloidogyne enterolobii control.Microbiome · 2025Article
- Biombalance™, an Oligomeric Procyanidins-Enriched Grape Seed Extract, Prevents Inflammation and Microbiota Dysbiosis in a Mice Colitis Model.Antioxidants (Basel, Switzerland) · 2025Article
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- Looking for Pathogens in Dust from North Africa Arriving in the French West Indies Using Metabarcoding and Cultivable Analysis.Microorganisms · 2024Article
- Investigating the Effect of Bacilli and Lactic Acid Bacteria on Water Quality, Growth, Survival, Immune Response, and Intestinal Microbiota of CulturedAnimals : an open access journal from MDPI · 2024Article
- A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data.Biochemical genetics · 2024Review
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- Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.International journal of molecular sciences · 2024Article
- UnveilingGut microbes · 2023Article
- Stevia as a natural additive on gut health and cecal microbiota in broilers.Veterinary and animal science · 2023Article
- Asterics: a simple tool for the ExploRation and Integration of omiCS data.BMC bioinformatics · 2023Article
- Article
- Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia.Viruses · 2023Article
- Antagonism of ALAS1 by the Measles Virus V protein contributes to degradation of the mitochondrial network and promotes interferon response.PLoS pathogens · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills.
resultsHere, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/ , and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman . Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis.
conclusionsWith SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.