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README.md
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## Introduction
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:
<img src="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 R 3.6.1. The installation, download and execution can all be performed with a small R script :
```
# Load shiny packages
if(!require('shiny')){
......
ui.R
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mainPanel(div(style = 'max-width: 900px',"docker pull aghozlane/shaman"),width=4,class="mainwell")
),
tabPanel("R install with Packrat",
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(),
"install.packages(c('devtools', 'codetools', 'lattice', 'MASS', 'survival', 'packrat'))", br(),
"library(devtools)",br(),"devtools::install_github(c('aghozlane/nlme'))", br(),
"# Download SHAMAN package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package.tar.gz"),width=9,class="mainwell"),
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(),
#"cd R-3.1.2/",br(), "./configure --prefix=/some/location/r_bin/", br(), "make && make install", br(), "/some/location/r_bin/bin/R", br(),
#"install.packages(c('devtools', 'codetools', 'lattice', 'MASS', 'survival', 'packrat'))", br(),
#"library(devtools)",br(),"devtools::install_github(c('aghozlane/nlme'))", br(),
"# Download SHAMAN package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_20190809.tar.gz"),width=9,class="mainwell"),
p("This installation will not interact with other R installation. Then, you can install SHAMAN with packrat:"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"# Install SHAMAN dependencies",br(),
"mkdir /some/location/shaman", br(), "/some/location/r_bin/bin/R",br(),
"install.packages(\"packrat\")",br(),"packrat::unbundle(\"shaman_package.tar.gz\", \"/packrat/location/shaman\")"), width=9,class="mainwell"),
"install.packages(\"packrat\")",br(),"packrat::unbundle(\"shaman_20190809.tar.gz\", \"/packrat/location/shaman\")"), width=9,class="mainwell"),
p("Now you can run SHAMAN:"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"library(packrat)",br(),"packrat::init(\"/packrat/location/shaman\")",br(),"library(shiny)",br(),
"system(\"Rscript -e 'library(\\\"shiny\\\");runGitHub(\\\"pierreLec/KronaRShy\\\",port=5438)'\",wait=FALSE)",
br(),"runGitHub('aghozlane/shaman')"),width=9,class="mainwell")),
tabPanel("R install (DEPRECATED)",
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"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"# Load shiny packages",br(),
"if(!require('shiny')){",br()," install.packages('shiny')",br()," library(shiny)",br(),"}",br(),
"system(\"Rscript -e 'library(\\\"shiny\\\");runGitHub(\\\"pierreLec/KronaRShy\\\",port=5438)'\",wait=FALSE)",
......
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