No lecture slides for this class. We’ll spend the entire time working on Step 1 script.

Homework: Introduction to the Tidyverse (~4hrs) - due before the start of class on March 6th.


We’ll begin this class by reviewing how to access R packages and help documentation, as well as understanding the basic structure of a script. We’ll then access annotation data before reading our Kallisto results into R. Our class concludes with discussing study design and using Sleuth for differentially transcript expression analysis.


  • Review basic elements of our scripts
  • Access annotation data using the Biomart package
  • View Kallisto results using Sleuth
  • Read Kallisto transcript abundance measurements into the R environment using TxImport


Step 1 script


Differential analysis of RNA-seq incorporating quantification uncertainty. Nature Methods, June, 2017 - Original paper describing Sleuth

Lior Pachter’s blog post on Sleuth

vignette for the Tximport package - the R package we’ll use to read the Kallisto mapping results into R.

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences* F1000Research, Dec 2015. This paper describes the Tximport package and its application for handling transcript-level expression measurments from lightweight aligners (Salmon, Sailfish, Kallisto)


Recorded lecture