SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, …). The statistical analysis performed by SHAMAN is based on DESeq2 R package Anders and Huber 2010 ] which robustly identifies the differential abundant features as suggested in McMurdie and Holmes 2014 and Jonsson2016. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 Love 2014. SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and generated figures can be downloaded in several formats. Hereafter is the global workflow of the SHAMAN application: