reproduce

Assessing the quality and reproducibility of absolute proteomic data. Companion repository to the pre-print "Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae".

This repository is administered by Benjamín J. Sánchez (@BenjaSanchez), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.

Requirements

R (tested with v3.6)
RStudio (tested with v1.2)
Rtools (in case of a windows setup)
Git (or any Git client of your choice, e.g. Github Desktop)

Installation

Clone locally this repository.
From the command window in RStudio, run each line in requirements.txt.

Usage

All analysis can be reproduced by knitting the RMarkdown file code/iBAQstudy.Rmd

Repository Structure

|- code/            # all programmatic code relating to the project
|  +- templates/    # scripts for generating template files
|
|- data/            # all data from the study
|  |- raw_internal/ # raw data generated in-lab or by collaborators, will not be altered
|  |- raw_external/ # data from third-party sources, databases etc, will not be altered
|     +- colormaps/ # color palettes used for all figures
|
|- doc/             # documentation for the study and other explanatory material
|  +- paper/        # contains the generated pdf from knitting the markdown file
|
|- results          # all output from workflows and analyses
|  |- figures/      # graphs, designated for manuscript figures
|  +- pictures/     # diagrams, images, and other non-graph graphics
|
|- .gitignore       # files that will not sync to Github
|- LICENSE          # license
|- README.md        # the top level description of content
|- reproduce.Rproj  # contains project information used to customize the behavior of RStudio  
+- requirements.txt # the requirements file for reproducing the analysis environment

Contributors

Kate Campbell (@KateCampbell87), Chalmers University of Technology, Sweden
Benjamín J. Sánchez (@BenjaSanchez), Chalmers University of Technology, Sweden

Acknowledgements

The initial file and directory structure of this project was developed by a group of participants in the Reproducible Science Curriculum Workshop, held at NESCent in December 2014. The structure is based on, and heavily follows the one proposed by Noble 2009, with a few but small modifications. The original repository has been modified to the reproducible-research-init repository and adapted to this project.