Overview
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Copy and paste the following code into the R script you just created, then run the code (highlight all the code in your R script, then press the run button). This will install all the required packages and dependencies and may take 45 minutes or more to complete. It may prompt you occasionally to update packages - select 'a' for all if/when this occurs.
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NOTE: you only need to run this section once if you’re running this analysis on your own laptop/PC, and you don’t need to run it if you’re using an rVDI machine as all the packages are already installed.
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#### Differential expressionMetagenomics analysis #### # When you see '## USER INPUT', this means you have to modify the code for your computer or dataset. All other code can be run as-is (i.e. you don't need to understand the code, just run it) #### 21. Installing required packages #### # **NOTE: this section only needs to be run once (or occasionally to update the packages) # Install devtools install.packages("devtools", repos = "http://cran.us.r-project.org") # Install R packages. This only needs to be run once. # Variannt calling Make a vector of CRAN and Bioconductor packages bioconductor_packages <- c("VariantAnnotation", "biomaRt", "clusterProfiler", "org.Hs.eg.db") cran_packages <- c("devtools", "tidyverse", "DT", "gt", "openxlsx", "dplyr", "scales", "ggplot2", "plotly", "tidyr", "ggsci", "viridis", "vcfR", "data.table", "remotes") # Compares Matagenomicsinstalled packages #to CRAN: library(tidyverse) library(scales) install.packages("remotes", verbose = F) remotes::install_github("MadsAlbertsen/ampvis2", quiet = T) library(ampvis2) # Bioconductor: bioconductor_packages <- c("DESeq2", "EnhancedVolcano", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "org.EcK12.eg.db", "org.EcSakai.eg.db", "org.Dr.eg.db", "org.Dm.eg.db") cran_packages <- c("ggrepel", "ggplot2", "plyr", "reshape2", "readxl", "FactoMineR", "factoextra", "pheatmap") # Compares installed packages to above packages and returns above packages and returns a vector of missing packages new_packages <- bioconductor_packages[!(bioconductor_packages %in% installed.packages()[,"Package"])] new_cran_packages <- cran_packages[!(cran_packages %in% installed.packages()[,"Package"])] # Install missing bioconductor packages if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(new_packages) # Install missing cran packages if (length(new_cran_packages)) install.packages(new_cran_packages, repos = "http://cran.us.r-project.org") # Update all installed packages to the latest version update.packages(bioconductor_packages, ask = FALSE) update.packages(cran_packages, ask = FALSE, repos = "http://cran.us.r-project.org") # Install ampvis2 (needs to be installed from Github) remotes::install_github("kasperskytte/ampvis2") |
3. Load required R packages
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