aghozlane/shaman repository overview

SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016] . SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014] . Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995]. The PCOA is performed with the ade4 R package and plots are generated with ggplot2 or D3.js packages .