# Core data manipulation and visualization
library(tidyverse) # Data manipulation and ggplot2
library(scales) # Axis scaling and transformations
library(ggtext) # Markdown text in ggplot2
library(ggpubr) # Publication-ready plots
library(ggrepel) # Non-overlapping text labels
library(ggh4x) # Extended ggplot2 features (faceting)
# Data export
library(writexl) # Writing Excel files
# Statistical modeling
library(lme4) # Linear mixed-effects models
library(lmerTest) # p-values for mixed models
library(emmeans) # Estimated marginal means and contrasts
# Data summary and tables
library(skimr) # Data summaries
library(knitr) # Table formatting with kable()
library(kableExtra) # Extended table formatting
library(gridExtra) # Arranging tables and plots
# Specialized analyses
library(mixOmics) # Multivariate analysis (PCA, PLS-DA)
library(vegan) # Ecological diversity (rarefaction curves)
# RNA-Seq specific
library(tximport) # Importing transcript quantification
library(DESeq2) # Differential expression analysis
library(ashr) # Adaptive shrinkage for effect size estimation
library(fgsea) # Fast gene set enrichment analysis
# Visualization utilities
library(RColorBrewer) # Color palettes
library(viridis) # Color palettes
library(Cairo) # High-quality graphics device
# Interactive visualizations
library(plotly) # Interactive plots
library(htmltools) # HTML widgets support
library(htmlwidgets) # Widget framework
# Graphics utilities
library(grid) # Low-level graphicsR 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
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 26.6.2
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 stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] htmlwidgets_1.6.4 htmltools_0.5.9
[3] plotly_4.12.0 Cairo_1.7-0
[5] viridis_0.6.5 viridisLite_0.4.3
[7] RColorBrewer_1.1-3 fgsea_1.34.2
[9] ashr_2.2-63 DESeq2_1.48.2
[11] SummarizedExperiment_1.38.1 Biobase_2.68.0
[13] MatrixGenerics_1.20.0 matrixStats_1.5.0
[15] GenomicRanges_1.60.0 GenomeInfoDb_1.44.3
[17] IRanges_2.42.0 S4Vectors_0.46.0
[19] BiocGenerics_0.54.1 generics_0.1.4
[21] tximport_1.36.1 vegan_2.7-2
[23] permute_0.9-8 mixOmics_6.32.0
[25] lattice_0.22-7 MASS_7.3-65
[27] gridExtra_2.3 kableExtra_1.4.0
[29] knitr_1.51 skimr_2.2.2
[31] emmeans_2.0.1 lmerTest_3.2-0
[33] lme4_2.0-1 Matrix_1.7-4
[35] writexl_1.5.4 ggh4x_0.2.8
[37] ggrepel_0.9.6 ggpubr_0.6.0
[39] ggtext_0.1.2 scales_1.4.0
[41] lubridate_1.9.4 forcats_1.0.1
[43] stringr_1.6.0 dplyr_1.2.0
[45] purrr_1.2.1 readr_2.1.6
[47] tidyr_1.3.2 tibble_3.3.1
[49] ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] rstudioapi_0.18.0 jsonlite_2.0.0 magrittr_2.0.4
[4] estimability_1.5.1 farver_2.1.2 nloptr_2.2.1
[7] rmarkdown_2.30 vctrs_0.7.2 minqa_1.2.8
[10] base64enc_0.1-6 SQUAREM_2021.1 mixsqp_0.3-54
[13] rstatix_0.7.3 S4Arrays_1.8.1 truncnorm_1.0-9
[16] broom_1.0.12 SparseArray_1.8.1 Formula_1.2-5
[19] plyr_1.8.9 igraph_2.2.1 lifecycle_1.0.5
[22] pkgconfig_2.0.3 R6_2.6.1 fastmap_1.2.0
[25] GenomeInfoDbData_1.2.14 rbibutils_2.4.1 digest_0.6.39
[28] numDeriv_2016.8-1.1 rARPACK_0.11-0 irlba_2.3.7
[31] RSpectra_0.16-2 textshaping_1.0.4 ellipse_0.5.0
[34] invgamma_1.2 timechange_0.4.0 httr_1.4.8
[37] abind_1.4-8 mgcv_1.9-4 compiler_4.5.1
[40] withr_3.0.2 backports_1.5.0 BiocParallel_1.42.2
[43] carData_3.0-6 ggsignif_0.6.4 DelayedArray_0.34.1
[46] corpcor_1.6.10 tools_4.5.1 otel_0.2.0
[49] glue_1.8.0 nlme_3.1-168 gridtext_0.1.6
[52] cluster_2.1.8.1 reshape2_1.4.5 gtable_0.3.6
[55] tzdb_0.5.0 data.table_1.18.2.1 hms_1.1.4
[58] xml2_1.5.2 car_3.1-5 XVector_0.48.0
[61] pillar_1.11.1 splines_4.5.1 tidyselect_1.2.1
[64] locfit_1.5-9.12 reformulas_0.4.4 svglite_2.2.2
[67] xfun_0.56 stringi_1.8.7 UCSC.utils_1.4.0
[70] lazyeval_0.2.2 yaml_2.3.12 boot_1.3-32
[73] evaluate_1.0.5 codetools_0.2-20 cli_3.6.5
[76] xtable_1.8-4 systemfonts_1.3.1 Rdpack_2.6.6
[79] repr_1.1.7 Rcpp_1.1.1 coda_0.19-4.1
[82] parallel_4.5.1 mvtnorm_1.3-3 crayon_1.5.3
[85] rlang_1.1.7 fastmatch_1.1-8 cowplot_1.1.3 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 fileThis command uses the renv.lock file to install the exact package versions required for the analysis.