SHAMAN is dedicated to metagenomic analysis, it includes the normalization, the differential analysis and mutiple visualization.
SHAMAN is based on DESeq2 R package [Anders and Huber 2010](http://www.ncbi.nlm.nih.gov/pubmed/20979621)for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/) and [Jonsson2016](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/).
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](http://www.ncbi.nlm.nih.gov/pubmed/20979621)] which robustly identifies the differential abundant features as suggested in [McMurdie and Holmes 2014](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/) and [Jonsson2016](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/).
SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014](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 ade4 R package and plots are generated with ggplot2 or D3.js packages.
A presentation about SHAMAN is available [here](www/shaman_presentation.pdf).
SHAMAN is compatible with standard formats for metagenomic analysis. We also provide a complete pipeline for OTU picking and annotation named [MASQUE](https://github.com/aghozlane/masque) used in production at Institut Pasteur.
Hereafter is the global workflow of the SHAMAN application:
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:
<imgsrc="www/Workflow.png"align="center"/>
## Installation
SHAMAN is available for R>3.1.2. The installation, download and execution can all be performed with a small R script :
SHAMAN is available for R3.6.1. The installation, download and execution can all be performed with a small R script :
p("SHAMAN is available for R=3.1.2. Packrat framework installation allow an easy installation of all the dependencies. Of note, raw data submission is not possible with this version. First, install R 3.1.2 as local install as follow:",style="font-family: 'times'; font-si16pt"),
mainPanel(div(style='max-width: 900px; word-wrap: break-word;',"# Install R 3.1.2",br(),
"wget https://pbil.univ-lyon1.fr/CRAN/src/base/R-3/R-3.1.2.tar.gz && tar -zxf R-3.1.2.tar.gz",br(),"mkdir /some/location/r_bin",br(),
"cd R-3.1.2/",br(),"./configure --prefix=/some/location/r_bin/",br(),"make && make install",br(),"/some/location/r_bin/bin/R",br(),
p("SHAMAN is available for R=3.6.1. Packrat framework installation allow an easy installation of all the dependencies. Of note, raw data submission is not possible with this version. First, install R 3.1.2 as local install as follow:",style="font-family: 'times'; font-si16pt"),
mainPanel(div(style='max-width: 900px; word-wrap: break-word;',"# Install R 3.6.1",br(),
#"wget https://pbil.univ-lyon1.fr/CRAN/src/base/R-3/R-3.1.2.tar.gz && tar -zxf R-3.1.2.tar.gz",br(),"mkdir /some/location/r_bin",br(),
p("SHAMAN is available for R=3.1.2. A more recent installation of R will break the differential abundance interface. The installation, download and execution can all be performed with a small R script:",style="font-family: 'times'; font-si16pt"),
tabPanel("R install",
p("SHAMAN is available for R=3.6.1. A more recent installation of R will break the differential abundance interface. The installation, download and execution can all be performed with a small R script:",style="font-family: 'times'; font-si16pt"),