In this brief workflow, we start with aligned featureCounts mapped at the gene-level and perform data pre-processing and exploratory analyses. Base R and the edgeR package are used to import, filter, and organize the raw counts data. We then finish off with data reduction visualizations and quality control checks. By doing so, this allows for ease in performing downstream differential expression analysis and gene set testing.
This pipeline is inspired by Law et al. 2018 and Justin Colacino's 'Komen plexwell processing.R' script (unpublished).
