vsmc-omics-postprocessing_quarto-renv-inputdata

Version 3 (latest)

• Version 3 (latest)
  
• Version 2
  
• Version 1 (earliest)
  

This archive contains all necessary files to reproduce the postprocessing and analysis pipeline for [ "omics data analysis in VSMCs"]. The workflow includes a Quarto report, a Conda environment specification (omics-vsmc-env), and input data used for the analysis. The environment ensures reproducibility across systems without requiring hardcoded paths.

Included files:

Postprocessing_no_cov_filter.qmd — The main Quarto report for data visualization and results.

renv.lock and renv/ — R environment snapshot to restore all R package dependencies.

omics-vsmc-env.yml — Defines the Conda environment including R, Quarto, and necessary system packages.

run_analysis.sh — A shell script to set up the environment and run the full pipeline non-interactively.

input_data

README.md — Instructions for setting up and executing the pipeline

Instructions:

1.Unzip the archive.

2.Create the Conda environment:

conda env create -f omics-vsmc-env.yml

3.Run the analysis:

./run_analysis.sh