Role of sex as a biological variable in neonatal alveolar macrophages PMID: 39098263

The book folder contains quarto files with a step by step analysis. The R folder conatins all of the functions used on each step.

GEO

GSE267573

Docker

The Docker BioContainer Image was used to run this analysis and can be found here: bioconductor_docker:3.18-R-4.3.2

How to run

R 4.3.2 and the package renv is recommended so the user can accurately replicate the resulsts in the publication.

Clone the project, download the raw counts (GSE267573_raw_counts.csv.gz) from GEO gunzip it and place on raw_data subfolder.

I like to create a new container using the image mentioned above and mounting the folder in my host machine to /home in the container. Then I attach visual studio code (with the R and quarto extensions installed) to the mounted folder (using the visual studio docker extension) and run the pipeline with these steps:

Install needed packages to run pipeline.

In the R console:

install.packages("renv")

renv::init() # Restore the project from the provided lockfile.

In the terminal:

quarto render book/

Questions & Comments

Please contact Abiud (the owner of this repo) for any questions or comments.