Installing ChemRICH

ChemRICH functions have been coded in R. It is expected that a user knows the basic usage of R scripting in the R-Studio software. But, most of the hard-work is actually preparing the input excel files for different ChemRICH analysis types.

Software requirements :

• R version > 4.0 (link)

• Latest RStudio (https://rstudio.com/ )

• Latest Java (www.java.com)

Operating system

• Windows 7 or 10 (tested)

• Should work on Linux and Mac OS (but not tested)

Install required R packages.

Run below R code to install the packages that ChemRICH scripts will need. Make sure your R version is > 4.0 and you have installed Java on your computer.

if (!require("devtools"))

install.packages('devtools', repos="http://cran.rstudio.com/")

if (!require("RCurl"))

install.packages('RCurl', repos="http://cran.rstudio.com/")

if (!require("pacman"))

install.packages('pacman', repos="http://cran.rstudio.com/")

library(devtools)

library(RCurl)

library(pacman)

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

pacman::p_load(GGally)

pacman::p_load(DT)

pacman::p_load(RCurl)

pacman::p_load(RJSONIO)

pacman::p_load(ape)

pacman::p_load(devEMF)

pacman::p_load(dynamicTreeCut)

pacman::p_load(extrafont)

pacman::p_load(ggplot2)

pacman::p_load(ggpubr)

pacman::p_load(ggrepel)

pacman::p_load(grid)

pacman::p_load(htmlwidgets)

pacman::p_load(igraph)

pacman::p_load(magrittr)

pacman::p_load(network)

pacman::p_load(officer)

pacman::p_load(openxlsx)

pacman::p_load(phytools)

pacman::p_load(plotly)

pacman::p_load(plotrix)

pacman::p_load(rcdk)

pacman::p_load(readxl)

pacman::p_load(rvg)

pacman::p_load(sna)

pacman::p_load(visNetwork)

Once you are done with installing the required R-packages you can do ahead and use different variants of the ChemRICH analysis. The first step is to understand the prepare the input file, for which instructions are provided here (LINK).