Bacterial Stress Responses Lower mRNA-Protein Level Correlations

Requirements

• R ≥ 4.4 — download from https://cran.r-project.org
• Rtools (Windows only) — must match your R version exactly. Download from https://cran.r-project.org/bin/windows/Rtools/

1 — Clone the repository

git clone https://github.com/avicanlab/RNAProtCorr
cd RNAProtCorr

2 — Restore the R environment with renv

This project uses renv to pin all package versions. Open R (or RStudio) in the project root and run:

install.packages("renv")
renv::restore()

Common issues

Problem	Solution
BiocParallel fails to compile	Update Rtools to match your R version, then re-run renv::restore()
A single package cannot be installed	Exclude it: renv::restore(exclude = "pkgName"), then install manually with install.packages() or BiocManager::install()
renv::restore() asks to activate — say yes	This links the project library so packages are isolated

3 — Download data from Zenodo

All raw data files are archived on Zenodo at https://zenodo.org/records/19488690.

Option A — R (recommended, reproducible)

# install.packages("zen4R")   # run once if not already installed
library(zen4R)

zenodo <- ZenodoManager$new()
record <- zenodo$getRecordByDOI("10.5281/zenodo.19488689")
# List available files in the record (to find the exact filename)
files <- record$listFiles()
print(files)


dir.create(file.path("DATA"), showWarnings = FALSE)

# Download the DATA archive
record$downloadFiles(
  files = "DATA_notebook.zip",  # exact filename
  path = "DATA"
)

unzip(
  zipfile = file.path("DATA", "DATA_notebook.zip"),
  exdir   = "DATA"
)

# Optional: remove the zip after extraction to save space
file.remove(file.path("DATA", "DATA_notebook.zip"))

Option B — Command line

# requires curl ≥ 7.x
data_notebook = "https://zenodo.org/records/19488690/files/DATA_notebook.zip?download=1"
curl -L "$data_notebook" -o $data_notebook.zip
unzip $data_notebook.zip -d DATA/

Option C — Browser

1. Open https://zenodo.org/records/19488690
2. Click Download for the DATA_notebook.zip archive.
3. Unzip into the DATA/ folder at the project root

Expected DATA folder structure

DATA/
├── Read_counts/          # RNA-seq TPM Excel files  (*.xlsx)
├── Proteome/             # TMT result TSV files, annotation, sample mapping
│   ├── sample_mapping.xlsx
│   ├── <Species>/
│   │   ├── annotation.xlsx
│   │   └── <Species>_R<n>.tsv
├── Fasta_files/          # Proteome FASTA files     (*.fa)
├── Essential genes/      # Essential gene lists     (*.xlsx)
├── Enrichment/           # GO term files            (*.xlsx / *.csv)
├── Stimulons/            # Stimulon gene lists      (*.xlsx)
└── ORA/                  # MOBILE framework output  (*.csv / *.txt)

4 — Render the notebook

rmarkdown::render("main.Rmd")

Or use the Knit button in RStudio.

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