RSVBac

Authors

Leah Kafer

Isabel F. Escapa

Published

October 27, 2026

Overview

This repository contains all analysis code and documentation for the manuscript:

Streptococcus pneumoniae colonization most strongly modulates human nasal epithelial responses to respiratory syncytial virus infection compared to Haemophilus influenzae or Dolosigranulum pigrum

Repository Structure and Data Availability

All analyses are provided as individual Quarto (.qmd) notebooks, which can be rendered independently. Each notebook reads processed .rds files from the dataframes/ folder and generates publication-quality figures and statistical outputs.

You can clone or download this repository to your local machine.

Setting Required Path Variable

Set the following environment variable in R before running notebooks:

Sys.setenv(BOX_PATH_RSVBacPublication = "/path/to/your_project")

Alternatively, add to your .Renviron file:

BOX_PATH_RSVBacPublication=/path/to/your_project

Reproducible R Environment with renv

This repository uses renv to ensure your R environment matches exactly with that used for manuscript analysis.

Setup Steps:

Install renv (if you don’t already have it): install.packages("renv")
From the project directory (with renv.lock present), restore all required package versions with: renv::restore()

This will install all necessary packages into a project-local library for full reproducibility.

Rendering the Project

You may render the entire project from the terminal:

quarto render

Or use “Render” or “Build” in RStudio.

Available Analysis Notebooks

1. Quantification of bacterial CFUs

2. RSV PFU quantification

3. RSV qRT-PCR quantification

4. Caspase Assay

5. RNASeq Analysis

6. Cytokine Analysis

Exploring the RNA-seq Results in CONTENTO

The RNASeq Analysis notebook also writes RSVbac_RNASeq_human_SE.rds, a SummarizedExperiment object with all the contrasts from the manuscript DESeq2 model. A copy is included in the SE/ folder of this repository. Upload it in CONTENTO (doi:10.5281/zenodo.21629492) to explore the results interactively; see the CONTENTO documentation for how to run the app.

# Overview {.unnumbered} ::: {.callout-note icon="false"} ## This repository contains all analysis code and documentation for the manuscript: ***Streptococcus pneumoniae*** **colonization most strongly modulates human nasal epithelial responses to respiratory syncytial virus infection compared to *Haemophilus influenzae* or *Dolosigranulum pigrum*** ::: ## Repository Structure and Data Availability All analyses are provided as individual Quarto (`.qmd`) notebooks, which can be rendered independently. Each notebook reads processed `.rds` files from the `dataframes/` folder and generates publication-quality figures and statistical outputs. You can clone or download this [repository](https://github.com/KLemonLab/RSVBac_Manuscript) to your local machine. ## Setting Required Path Variable Set the following environment variable in R before running notebooks: ``` Sys.setenv(BOX_PATH_RSVBacPublication = "/path/to/your_project") ``` Alternatively, add to your `.Renviron` file: ``` BOX_PATH_RSVBacPublication=/path/to/your_project ``` ## Reproducible R Environment with renv This repository uses [`renv`](https://rstudio.github.io/renv/) to ensure your R environment matches exactly with that used for manuscript analysis. **Setup Steps:** 1. Install renv (if you don't already have it): ``` install.packages("renv") ``` 2. From the project directory (with `renv.lock` present), restore all required package versions with: ``` renv::restore() ``` This will install all necessary packages into a project-local library for full reproducibility. ## Rendering the Project You may render the entire project from the terminal: ``` quarto render ``` Or use “Render” or “Build” in RStudio. ## Available Analysis Notebooks 1\. [Quantification of bacterial CFUs](Manuscript_RSVbac_CFUs.html) 2\. [RSV PFU quantification](Manuscript_RSVbac_PFUs.html) 3\. [RSV qRT-PCR quantification](Manuscript_RSVbac_ViralTiters.html) 4\. [Caspase Assay](Manuscript_RSVbac_Caspase.html) 5\. [RNASeq Analysis](Manuscript_RSVbac_RNASeqHNOs.html) 6\. [Cytokine Analysis](Manuscript_RSVbac_Cytokines.html) ## Exploring the RNA-seq Results in CONTENTO The [RNASeq Analysis](Manuscript_RSVbac_RNASeqHNOs.html#contento-summarizedexperiment) notebook also writes `RSVbac_RNASeq_human_SE.rds`, a SummarizedExperiment object with all the contrasts from the manuscript DESeq2 model. A copy is included in the `SE/` folder of this repository. Upload it in [CONTENTO](https://github.com/KLemonLab/CONTENTO) ([doi:10.5281/zenodo.21629492](https://doi.org/10.5281/zenodo.21629492)) to explore the results interactively; see the [CONTENTO documentation](https://klemonlab.github.io/CONTENTO/) for how to run the app.