". SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2",a("[Love 2014]",href="http://www.ncbi.nlm.nih.gov/pubmed/25516281"),".
Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995].
The PCOA is performed with the",a("ade4 R package",href="http://pbil.univ-lyon1.fr/ade4/"),"and plots are generated with",a("ggplot2",href="http://ggplot2.org/"),"or",a("D3.js packages",href="http://d3js.org/"),".
A presentation about SHAMAN is available",a("here.",target="_blank",href="shaman_presentation.pdf"),br(),
A presentation about SHAMAN is available",a("here",target="_blank",href="shaman_presentation.pdf")," and a poster",a("here.",target="_blank",href="shaman_poster.pdf"),br(),
"SHAMAN is compatible with standard formats for metagenomic analysis. We also provide a complete pipeline for OTU picking and annotation named",a("MASQUE",href="https://github.com/aghozlane/masque"),"used in production at Institut Pasteur.",style="font-family: 'times'; font-si16pt"),
p("Hereafter is the global workflow of the SHAMAN application:"),