R Session Info

This document lists all R packages used across analysis notebooks in this repository, and details how to reproduce or create similar analysis environments.

Package Loading

library(tidyverse)      # Data manipulation and ggplot2
library(ggtext)         # Markdown text in ggplot2
library(viridis)        # Color palettes
library(RColorBrewer)   # Color palettes
library(knitr)          # Dynamic report generation
library(ggh4x)          # Extensions for ggplot2
library(cowplot)        # Plot arrangement
library(png)            # Reading PNG images
library(grid)           # Grid graphics
library(reshape2)       # Data reshaping
library(seqinr)         # Reading and writing FASTA files

Session Information

This shows the exact versions of R and all packages used in the analysis.

sessionInfo()

R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Tahoe 26.3.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] grid      stats     graphics  grDevices datasets  utils     methods  
[8] base     

other attached packages:
 [1] seqinr_4.2-36      reshape2_1.4.5     png_0.1-8          cowplot_1.1.3     
 [5] ggh4x_0.2.8        knitr_1.51         RColorBrewer_1.1-3 viridis_0.6.5     
 [9] viridisLite_0.4.3  ggtext_0.1.2       lubridate_1.9.4    forcats_1.0.1     
[13] stringr_1.6.0      dplyr_1.2.0        purrr_1.2.1        readr_2.1.6       
[17] tidyr_1.3.2        tibble_3.3.1       ggplot2_3.5.1      tidyverse_2.0.0   

loaded via a namespace (and not attached):
 [1] generics_0.1.4      renv_1.1.7          xml2_1.5.2         
 [4] stringi_1.8.7       hms_1.1.4           digest_0.6.39      
 [7] magrittr_2.0.4      evaluate_1.0.5      timechange_0.4.0   
[10] fastmap_1.2.0       plyr_1.8.9          jsonlite_2.0.0     
[13] gridExtra_2.3       BiocManager_1.30.27 scales_1.4.0       
[16] ade4_1.7-23         cli_3.6.5           rlang_1.1.7        
[19] withr_3.0.2         yaml_2.3.12         tools_4.5.1        
[22] tzdb_0.5.0          vctrs_0.7.2         R6_2.6.1           
[25] lifecycle_1.0.5     MASS_7.3-65         pkgconfig_2.0.3    
[28] pillar_1.11.1       gtable_0.3.6        glue_1.8.0         
[31] Rcpp_1.1.1          xfun_0.56           tidyselect_1.2.1   
[34] rstudioapi_0.18.0   farver_2.1.2        htmltools_0.5.9    
[37] rmarkdown_2.30      compiler_4.5.1      gridtext_0.1.6     

Reproducibility and Environment

This repository manages R package versions using renv.

To reproduce the environment for this project:

#renv::init() # Was used to create the initial renv environment and lockfile
#renv::snapshot() # Was used to update the renv.lock file after installing new packages
#renv::restore() # Restores the R environment based on the renv.lock file

This command uses the renv.lock file to install the exact package versions required for the analysis.