RNA-seq analysis (RNA123 workflow)

Data packaging

• Reading in count-data
• Organizing sample imformation
• Organizing gene annotations

Data preprocessing

• Transformations from the raw-scale
• Removing genes that are lowly expressed
• Normalising gene expression distributions
• Unsupervised clustering of samples

Differential expression analysis

• Creating a design matrix and contrasts
• Removing heteroscedascity from count data
• Examining the number of DE genes
• Examining individual DE genes from top to bottom
• Useful graphical representations of differential expression results