Technical report: variability in glycopeptide workflow

This repository contains files used in the creation of a report on the variability in glycopeptide intensity. The report describes joint work by Frania J. Zuñiga-Bañuelos and Maarten van Schaik, PhD candidates in the EU-funded programme IMforFUTURE (Innovative training in methods for future data).

The report can be read here: N-glycoproteomics-workflow-variability/.

For the statistical part in the report, the following software was used:

• R version 3.6.3 (2020-02-29) 64-bit
• Tableau 2020.2

The following R packages were used:

• Tidyverse 1.3.0
• readxl 1.3.1
• writexl 1.3
• ggplot2 3.3.0
• data.table 1.12.8

The files are:

Data files:

• /data/Fib_1.csv-Fib_4.csv: The raw data.
• /data/Fib_total_processed.csv: Merged and pre-processed raw data.
• /data/Fib_total_processed.Rds: Merged and pre-processed raw data in RDs form.
• /data/summaries/Fib_summary_AUC.xlsx: Summary measures of N-glycopeptide intensities per replicate and mean, sd and CV of these.
• /data/summaries/Fib_summary_count.xlsx: Summary measures of N-glycopeptide counts, relative counts and presence indicators per replicate and mean, sd and CV of these.

Figures:

• /Figures/

Scripts

• /scripts/R/N-glycopeptide Statistical Analysis.Rmd: All R scripts.
• /scripts/Tableau/Fib_4_samples.twbx: Tableau Packaged Workbook for visualisations.

Blog post / report files:

• index.Rmd and index.html: Files to build the website for the report.