A compendium of scripts and analysis for Lee, Zhang et. al, 2019
using superintronic, including supplementary information.
Other scripts and analyses are available as part of https://github.com/charitylaw/intron-reads
The project is laid out as an R package using the following directory structure:
data/(cached data, saved from Rmd and R scripts, includes kallisto results)Rmd/(reports for each part of the analysis)R/(functions used to create "pretty" coverage plots)img/(all figures created during analyses; including supp figures)scripts/(batch processing of raw data files, and scripts to reproduce figures)
You can install all the analysis dependencies using:
# install.packages("BiocManager")
BiocManager::install("sa-lee/analysis-superintronic")
Note that you will need to have git-lfs installed if you would like to use the cached data directly.