periscope-publication

This repository contains all supplementary data files and code required to re-create most* of the figures in:

periscope: sub-genomic RNA identification in SARS-CoV-2 Genomic Sequencing Data

Matthew D Parker, Benjamin B Lindsey, Shay Leary, Silvana Gaudieri, Abha Chopra, Matthew Wyles, Adrienn Angyal, Luke R Green, Paul Parsons, Rachel M Tucker, Rebecca Brown, Danielle Groves, Katie Johnson, Laura Carrilero, Joe Heffer, David Partridge, Cariad Evans, Mohammad Raza, Alexander J Keeley, Nikki Smith, Ana Da Silva Filipe, James Shepherd, Chris Davis, Alain Kohl, Elihu Aranday-Cortes, Lily Tong, Emma C Thomson, Dennis Wang, Simon Mallal, Thushan I de Silva

Requirements:

• R 3.5.0 or greater with the following packages installed:

  • ggplot2
  • reshape2
  • scales
  • tidyverse
  • ftplottools
  • viridis
  • ggsignif
  • ggpubr
  • GGally
  • FactoMineR
  • factoextra
  • png
  • scales

• most refers to the fact that some figures have been produced with IGV/Adobe Illustrator. Where there are mixed figures, the IGV pots have been provided as images which are added to the figures with ggarrange.