Extraction

This repository contains the code and result images accompanying the paper:

Systematic Comparison of Bone Proteome Extraction Methods to Allow for Integrated Proteomics-Metabolomics-Correlation

Overview

• Result Images: The results directory contains the figures and supplementary images generated for the paper.
• R Markdown File: The .Rmd file (Workflow.Rmd) allows you to run the code used in the analysis and recreate the result images.
• Environment: The corresponding computational environment required to run the code can be found as a Docker image on Docker Hub.

Running the Analysis

To recreate the result images:

1. Ensure you have R and the required environment configured. Using the Docker image is recommended for reproducibility.
2. Run the Workflow.Rmd file in your R setup or RStudio.

Docker Environment

The computational environment for running the code is available on Docker Hub:

• Docker Hub Repository: kadam0/extraction_prot
• Tags:
  • rstudio: Provides a GUI-based environment with RStudio.
  • r: Allows running the code in a terminal-based R environment.

Using the Docker Environment

1. Pull the Docker image:

   docker pull kadam0/extraction_prot:rstudio

2. Run the container:

   docker run -p 8787:8787 -e PASSWORD=yourpassword kadam0/extraction_prot:rstudio

3. Access RStudio in your browser at http://localhost:8787 and run Workflow.Rmd.

Citation

If you use this repository or the Docker environment, please cite the associated paper:

Systematic Comparison of Bone Proteome Extraction Methods to Allow for Integrated Proteomics-Metabolomics-Correlation.

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For any issues or questions, feel free to contact the repository maintainers or refer to the paper for detailed