#options(download.file.method = 'wget', bitmapType='cairo') options(bitmapType='cairo') if (!require("Rcpp")){ install.packages("Rcpp", repos="http://cran.univ-paris1.fr/") } if(!require(shiny)){ install.packages("shiny", repos="http://cran.univ-paris1.fr/") library(shiny) } if(!require(shinydashboard)){ devtools::install_github('aghozlane/shinydashboard') library(shinydashboard) } if(!require(rjson)){ install.packages('rjson', repos="http://cran.univ-paris1.fr/") library(rjson) } if(!require(ape)){ install.packages('ape', repos="http://cran.univ-paris1.fr/") library(ape) } if(!require(GUniFrac)){ install.packages('GUniFrac', repos="http://cran.univ-paris1.fr/") library(GUniFrac) } if(!require(devtools)){ install.packages('devtools', repos="http://cran.univ-paris1.fr/") library(devtools) } if (!require(psych)) { install.packages('psych', repos="http://cran.univ-paris1.fr/") library(psych) } if (!require(ggplot2)) { install.packages('ggplot2', repos="http://cran.univ-paris1.fr/") library(ggplot2) } if (!require(vegan)) { install.packages('vegan', repos="http://cran.univ-paris1.fr/") library(vegan) } if (!require(dendextend)) { install.packages('dendextend', repos="http://cran.univ-paris1.fr/") library(dendextend) } if (!require(circlize)) { install.packages('circlize', repos="http://cran.univ-paris1.fr/") library(circlize) } if (!require(devtools)) { install.packages('devtools', repos="http://cran.univ-paris1.fr/") library(devtools) } if(!require(treeWeightD3)){ devtools::install_github('pierreLec/treeWeightD3') library(treeWeightD3) } if (!require(BiocInstaller)){ source("https://bioconductor.org/biocLite.R") biocLite("BiocInstaller") library(BiocInstaller) } if (!require(d3heatmap)) { devtools::install_github('aghozlane/d3heatmap') library(d3heatmap) } # Let us use biomformat instead of biom if (!require(biomformat)){ devtools::install_github("aghozlane/biomformat") library(biomformat) } if (!require(scatterD3)) { #devtools::install_github('aghozlane/scatterD3') install.packages("scatterD3") library(scatterD3) } if (!require(rNVD3)) { devtools::install_github('aghozlane/rNVD3') library(rNVD3) } if (!require(genefilter)) { source("https://bioconductor.org/biocLite.R") biocLite("genefilter") library(genefilter) } if (!require(googleVis)) { install.packages('googleVis', repos="http://cran.univ-paris1.fr/") suppressPackageStartupMessages(library(googleVis)) } if (!require(shinyjs)) { install.packages('shinyjs', repos="http://cran.univ-paris1.fr/") library(shinyjs) } if(!require(d3vennR)){ devtools::install_github("timelyportfolio/d3vennR") library(d3vennR) } if (!require(DT)) { install.packages('DT', repos="http://cran.univ-paris1.fr/") library(DT) } if (!require(RColorBrewer)) { install.packages('RColorBrewer', repos="http://cran.univ-paris1.fr/") library(RColorBrewer) } if (!require(gplots)) { install.packages('gplots', repos="http://cran.univ-paris1.fr/") library(gplots) } if (!require(DESeq2)) { devtools::install_github("aghozlane/DESeq2shaman") library(DESeq2) } if (!require(ade4)) { install.packages('ade4', repos="http://cran.univ-paris1.fr/") library(ade4) } if (!require(scales)) { install.packages('scales', repos="http://cran.univ-paris1.fr/") library(scales) } if (!require(phytools)) { install.packages('phytools', repos="http://cran.univ-paris1.fr/") library(phytools) } if(!require(philentropy)){ install.packages("philentropy", repos="http://cran.univ-paris1.fr/") library(philentropy) } if(!require(PhyloTreeMetaR)){ devtools::install_github("pierreLec/PhyloTreeMetaR") library(PhyloTreeMetaR) } if (!require("shinytoastr")){ devtools::install_github("mangothecat/shinytoastr") library(shinytoastr) } if (!require("shinyWidgets")){ devtools::install_github("aghozlane/shinyWidgets") library(shinyWidgets) } if (!require("sendmailR")){ install.packages("sendmailR", repos="http://cran.univ-paris1.fr/") library(sendmailR) } if (!require("shinyBS")){ install.packages("shinyBS", repos="http://cran.univ-paris1.fr/") library(shinyBS) } library(tools) if (!require("flexdashboard")){ install.packages("flexdashboard", repos="http://cran.univ-paris1.fr/") library(flexdashboard) } if (!require("backports")){ install.packages("backports", repos="http://cran.univ-paris1.fr/") library(backports) } if (!require("readr")){ install.packages("readr", repos="http://cran.univ-paris1.fr/") library(readr) } if (!require("jsonlite")){ install.packages("jsonlite", repos="http://cran.univ-paris1.fr/") library(jsonlite) } if (!require("shinyFiles")){ install.packages("shinyFiles", repos="http://cran.univ-paris1.fr/") library(shinyFiles) } if (!require("htmltools")){ install.packages("htmltools", repos="http://cran.univ-paris1.fr/") library(htmltools) } # if (!require("V8")){ # install.packages("V8", repos="http://cran.univ-paris1.fr/") # library(htmltools) # } # if(!require(plotly)){ # install.packages("plotly") # library(plotly) # } if (!require("rAmCharts")){ install.packages("rAmCharts") library(rAmCharts) } if(!require("colourpicker")){ install.packages("colourpicker") library(colourpicker) } if(!require("data.table")){ install.packages("data.table") library(data.table) } if(!require("UpSetR")){ install.packages("UpSetR") library(UpSetR) } if(!require("ggrepel")){ install.packages("ggrepel") library(ggrepel) } # if(!require("networkD3")){ # install.packages("networkD3") # library(networkD3) # } if(!require("igraph")){ install.packages("igraph") library(igraph) } if(!require("visNetwork")){ install.packages("visNetwork") library(visNetwork) }