Commit a3e337da authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

More description in the documentation

parent e31e6638
......@@ -152,7 +152,9 @@ body <- dashboardBody(
For one given contrast, we have:",br(),
"- The id of the given taxonomical level",br(),
"- The base mean is the mean normalized count for the given annotation of all samples.",br(),
"- The fold change .",br(),
"- The fold-change is a mesure describing how much the abundance varies from one condition to an other. For instance, if the abundance is 100 in condition 1 and 200 for condition 2, the fold-change equals 100/200=0.5.",br(),
"- The log2 fold-change is the log2 value of the fold-change.",br(),
"- The p-value adjusted (padj) is the pvalue obtained by the Wald test and adjusted by Benjamini & Hochberg procedure (BH) or Benjamini & Yekutieli procedure (see linear model options).",
img(src = "tutorial/tutorial_table.png",width = "100%",style="max-width: 900px"))),
tabPanel("5-Visualization",
p("'Diagnostic plots' section provides several visualization to control the analysis",br(),
......@@ -194,17 +196,20 @@ body <- dashboardBody(
tabBox(title="Download / Install SHAMAN", id="tabset1", width=NULL,
tabPanel("Docker install", tags$script(type="text/javascript", language="javascript", src="google-analytics.js"),
p("Docker install is the easiest way to use SHAMAN locally.",style = "font-family: 'times'; font-si16pt"),
p("- Install docker on Linux:"),
wellPanel("sudo apt-get install docker",br(),
"sudo service docker start"),
p("- Install docker on Windows and Mac"),
p("Docker install is the easiest way to use SHAMAN locally."),
p("- Install docker on ubuntu (Linux):",a("here",href="https://docs.docker.com/engine/installation/linux/ubuntulinux/")),
p("- Install docker on Windows and Mac:"),
p("Download and install docker from",a("https://www.docker.com/", href="https://www.docker.com/"),
"Then, you will need to install the", a("Docker toolbox.", href="https://www.docker.com/products/docker-toolbox"),
"Once installed, run ‘Docker Quickstart Terminal’ application."),
p("- Running SHAMAN:"),
wellPanel(div(style = 'width: 400px',"docker run --rm -p 80:80 aghozlane/shaman")),
p("Then connect to http://0.0.0.0/ with your favorite web navigator.")
p("Then connect to http://0.0.0.0/ with your favorite web navigator."),
p("Failed: port is already allocated ?"),
wellPanel(div(style = 'width: 400px',"docker run --rm -p 3838:80 aghozlane/shaman")),
p("Then connect to http://0.0.0.0:3838/."),
p("- Docker update after an update of SHAMAN:"),
wellPanel("docker pull aghozlane/shaman")
),
tabPanel("R install (RC)", tags$script(type="text/javascript", language="javascript", src="google-analytics.js"),
p("SHAMAN is available for R>3.1.2. The installation, download and execution can all be performed with a small R script :",style = "font-family: 'times'; font-si16pt"),
......
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