Get Started with C3NA

Kuncheng Song

3/15/2022

Source: vignettes/C3NA.Rmd

Step 1. Install R and R Studio

To run the application locally, you are required to install R and R Studio. C3NA was built under the following versions:

Step 2 Check if all dependent packages are installed properly 

## CRAN Repo
.cran_packages <- c("stringr", "tibble", "dplyr", "readr", "stats", "visNetwork", 
                    "igraph", "scales", "magrittr", "tidyr", "randomcoloR", 
                    "ggpubr", "ggplot2",  "plotly", "colorspace", 
                    "reshape2", "shiny", "shinyWidgets", "shinydashboard", 
                    "shinyjs", "reactable", "DT", "pheatmap", "dynamicTreeCut", 
                    "cluster", "WGCNA", "RColorBrewer", "base64enc", "htmlwidgets",
                    "foreach")
.inst <- .cran_packages %in% installed.packages()
if (any(!.inst)){
  install.packages(.cran_packages[!.inst],repos = "http://cran.rstudio.com/",
                   dependencies = TRUE)
}

## Bioconductor Repo
.bioc_packages <- c("phyloseq", "qvalue", "impute", 'GO.db', 'preprocessCore')
.inst <- .bioc_packages %in% installed.packages()
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
if(any(!.inst)){
  BiocManager::install(.bioc_packages[!.inst])
}
## GitHub Repo
.git_packages <- c("SpiecEasi", "metagMisc")
.git_packagesPath <- c("zdk123/SpiecEasi", "vmikk/metagMisc")
.inst <- .git_packages %in% installed.packages()
if (any(!.inst)){
  devtools::install_github(.git_packagesPath[!.inst])
}

Once the required package check is complete, you will be able to use C3NA package, and please check out a full tutorials with demo under Articles tab on the top guide bar.

Step 3. Install from Github 

# install.packages("devtools")
library(devtools)
install_github("zhouLabNCSU/C3NA")

Step 4. Package Check 

library(C3NA)
#> 
C3NAPackageCheck()
#>    Found      Library Version    PackageName
#> 1   TRUE         CRAN   1.4.0        stringr
#> 2   TRUE         CRAN   3.1.8         tibble
#> 3   TRUE         CRAN   1.0.9          dplyr
#> 4   TRUE         CRAN   2.1.2          readr
#> 5   TRUE         CRAN   4.1.0          stats
#> 6   TRUE         CRAN   2.1.0     visNetwork
#> 7   TRUE         CRAN   1.3.4         igraph
#> 8   TRUE         CRAN   1.2.1         scales
#> 9   TRUE         CRAN   2.0.3       magrittr
#> 10  TRUE         CRAN   1.2.0          tidyr
#> 11  TRUE         CRAN 1.1.0.1    randomcoloR
#> 12  TRUE         CRAN   0.4.0         ggpubr
#> 13  TRUE         CRAN   3.3.6        ggplot2
#> 14  TRUE         CRAN  4.10.0         plotly
#> 15  TRUE         CRAN   2.0.3     colorspace
#> 16  TRUE         CRAN   1.4.4       reshape2
#> 17  TRUE         CRAN   1.7.2          shiny
#> 18  TRUE         CRAN   0.7.3   shinyWidgets
#> 19  TRUE         CRAN   0.7.2 shinydashboard
#> 20  TRUE         CRAN   2.1.0        shinyjs
#> 21  TRUE         CRAN   0.3.0      reactable
#> 22  TRUE         CRAN    0.25             DT
#> 23  TRUE         CRAN  1.0.12       pheatmap
#> 24  TRUE         CRAN  1.63.1 dynamicTreeCut
#> 25  TRUE         CRAN   2.1.2        cluster
#> 26  TRUE         CRAN    1.71          WGCNA
#> 27  TRUE         CRAN   1.1.3   RColorBrewer
#> 28  TRUE         CRAN   0.1.3      base64enc
#> 29  TRUE         CRAN   1.5.4    htmlwidgets
#> 30  TRUE         CRAN   1.5.2        foreach
#> 31  TRUE Bioconductor  1.36.0       phyloseq
#> 32  TRUE Bioconductor  2.24.0         qvalue
#> 33  TRUE Bioconductor  1.66.0         impute
#> 34  TRUE       GitHub   1.1.2      SpiecEasi
#> 35  TRUE       GitHub   0.0.4      metagMisc

Because of the interactive R Shiny environment, C3NA required a large number of packages to be installed. Please run the following function to check if all packages are successfully installed. The function will output a table, and please make sure the column under “Found” are all TRUE