Workshop Description

RNA-seq II aims to provide tools for analysis of gene expression data from read counts to biology using R. To facilitate learning, the workshop will use a real case study based approach appropriate for Illumina read data (same as RNA-seq I).

From gene expression to biology (gene expression analysis):

  • Normalization of gene expression
  • Exploratory analysis of RNA-Seq data
  • Differential gene expression analysis
  • Gene set and pathway enrichment analysis
  • Visualization of gene expression

Technical Requirements

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
  • R:
  • R Studio:
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.


Alice Mouton, Ph.D., is an Assistant Project Scientist in Robert Wayne laboratory in the department of Ecology and Evolutionary Biology. Her current researches focus on applying gene expression methodologies (RNA-seq and RRBS) to study non model organisms (bobcat, island fox) in a context of conservation. Email:

Yerbol Kurmangaliev, Ph.D., is currently a postdoctoral researcher in the laboratory of Professor S. Lawrence Zipursky. He earned a M.S. degree in Biochemistry at Lomonosov Moscow State University in 2006. He earned a Ph.D. degree in Bioinformatics at Kharkevich Institute for information transmission problems of the Russian Academy of Sciences in 2011 under the supervision of Professor Mikhail S. Gelfand. Before joining to UCLA he was a postdoctoral researcher in the laboratory of Professor Sergey V. Nuzhdin at USC. His previous research interests have been primarily focused on genetic basis of gene expression. Email:


I learnt a lot of basic concepts and practical tools like PC plot form this workshop. The overview of the different normalization methods was most helpful. Thank you for the excellent workshop and keep up the great work!

Fall 2018 Student
It was nice that I could just copy and paste the scripts in case I missed real-time typing.
Winter 2018 Student

Very well organized, concise, and clear. I also thought it was helpful that instructor wrote the code out during class and explained what each part does. It made the class easy to follow.

Winter 2018 Student
Yerbel was great- I liked his approach of going through the analysis with us and walking through the steps. Thank you!!
Winter 2018 Student
Alice is a great instructor and communicated complex concepts clearly. I have taken several collaborator classes and this was the easiest one to follow and keep up with. She also used her time efficiently and was very organized, which I am grateful for. Thanks for a great class!
Fall 2017 Student

Workshop Details

Prerequisites: W3
Recommended: W5a
Length: 2 days, 2 hrs per day
Level: Intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Spring 2019 Dates

May 7 and 9, 2019
1:30 PM – 3:30 PM