LoadPackages.R 3.53 KB
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options(download.file.method = 'wget')

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if (!require("sendmailR")){
  install.packages("sendmailR")
  library(sendmailR)
}

if (!require("shinyBS")){
  install.packages("shinyBS")
  library(shinyBS)
}

library(tools)

if (!require("flexdashboard")){
  install.packages("flexdashboard")
  library(flexdashboard)
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}
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if (!require("backports")){
  install.packages("backports")
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  library(backports)
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}

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if (!require("readr")){
  install.packages("readr")
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  library(readr)
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}

if (!require("jsonlite")){
  install.packages("jsonlite")
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  library(jsonlite)
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}


if (!require("shinyFiles")){
  install.packages("shinyFiles")
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  library(shinyFiles)
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}


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if (!require("Rcpp")){
  install.packages("Rcpp")
}
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if(!require(shiny)){
  install.packages("shiny")
  library(shiny)
}
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if(!require(shinydashboard)){
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  devtools::install_github('aghozlane/shinydashboard')
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  library(shinydashboard)
}

if(!require(rjson)){
  install.packages('rjson')
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  library(rjson)
}
if(!require(ape)){
  install.packages('ape')
  library(ape)
}

if(!require(GUniFrac)){
  install.packages('GUniFrac')
  library(GUniFrac)
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}

if(!require(devtools)){
  install.packages('devtools')
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  library(devtools)
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}

if (!require(psych)) {
  install.packages('psych')
  library(psych)
}

if (!require(ggplot2)) {
  install.packages('ggplot2')
  library(ggplot2)
}

if (!require(vegan)) {
  install.packages('vegan')
  library(vegan)
}

if (!require(dendextend)) {
  install.packages('dendextend')
  library(dendextend)
}

if (!require(circlize)) {
  install.packages('circlize')
  library(circlize)
}


if (!require(devtools)) {
  install.packages('devtools')
  library(devtools)
}
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if(!require(treeWeightD3)){
   devtools::install_github('pierreLec/treeWeightD3')
   library(treeWeightD3)
}
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if (!require(BiocInstaller)){
  source("https://bioconductor.org/biocLite.R")
  biocLite("BiocInstaller")
  library(BiocInstaller)
}
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if (!require(d3heatmap)) {
  devtools::install_github('aghozlane/d3heatmap')
  library(d3heatmap)
}

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# Let us use biomformat instead of biom
if (!require(biomformat)){
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 devtools::install_github("aghozlane/biomformat")
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library(biomformat)
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}

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if (!require(scatterD3)) {
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  devtools::install_github('aghozlane/scatterD3')
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  library(scatterD3)
}

if (!require(rNVD3)) {
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  devtools::install_github('aghozlane/rNVD3')
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  library(rNVD3)
}

if (!require(genefilter)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("genefilter")
  library(genefilter)
}

if (!require(googleVis)) {
  install.packages('googleVis')
  suppressPackageStartupMessages(library(googleVis))
}

if (!require(shinyjs)) {
  install.packages('shinyjs')
  library(shinyjs)
}

if(!require(d3vennR)){
  install_github("timelyportfolio/d3vennR")
  library(d3vennR)
}

if (!require(DT)) {
  install.packages('DT')
  library(DT)
}

if (!require(RColorBrewer)) {
  install.packages('RColorBrewer')
  library(RColorBrewer)
}

if (!require(gplots)) {
  install.packages('gplots')
  library(gplots)
}

if (!require(DESeq2)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("DESeq2")
  library(DESeq2)
}

if (!require(ade4)) {
  install.packages('ade4')
  library(ade4)
}

if (!require(scales)) {
  install.packages('scales')
  library(scales)
}
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if (!require(phytools)) {
  install.packages('phytools')
  library(phytools)
}

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if(!require(philentropy)){
  devtools::install_github("HajkD/philentropy", build_vignettes = TRUE, dependencies = TRUE)
  library(philentropy)
}
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if(!require(PhyloTreeMetaR)){
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  devtools::install_github("pierreLec/PhyloTreeMetaR")
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  library(PhyloTreeMetaR)
}

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# if(!require(plotly)){
#   install.packages("plotly")
#   library(plotly)  
# }
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