Workshop Description (Intermediate Course)

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

Workshop Topics

Slides for RNAseq II- Day 1

Slides for RNAseq II- Day 2

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.


Dr. Karolina E. Kaczor-Urbanowicz, DMD, Phd, MSc is an Assistant Project Scientist in Prof. David Wong’s laboratory of UCLA Center for Oral/Head & Neck Oncology Research and Salivary Diagnostics, Section of Oral Biology, UCLA School of Dentistry. She is a dentist-scientist who graduated from the Faculty of Dental Medicine at the Medical University of Warsaw, Poland. She did her residency in orthodontics simultaneously with the international studies in Bio-Medical Sciences at the Hebrew University of Jerusalem, Israel, working in the Prof. Aaron Palmon’s Laboratory of Proteomics and Salivary Diagnostics, Institute of Dental Sciences. After earning her Ph.D. title, she was awarded the UCLA’s R90 NIH/NIDCR Postdoctoral Dentist-Scientist Scholarship and AACR-DDF postdoctoral fellowship in developing salivary H.pylori exRNA biomarkers for early detection of gastric cancer. At the UCLA, she developed her immense interests in salivary RNA Sequencing, bioinformatics and biomarker development for many oral and systematic diseases including cancer. Email:

Dr. Lingyun (Ivy) Xiong is a postdoctoral fellow at UCLA, working with Dr. Eric J. Deeds and Dr. Alan Garfinkel’s lab. Ivy focuses on dynamic processes in development, physiology, and cancer, with a special interest in the role of dynamic regulation in health and disease by applying techniques from nonlinear dynamics, computational biology and quantitative imaging. Her research aims to explain the spatiotemporal nature of diverse biological phenomena. Ivy completed her B.Sc. at the University of Hong Kong and earned her D.Phil. from the University of Oxford.



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!

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

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.

The class was great- I liked his approach of going through the analysis with us and walking through the steps. Thank you!!
The instructor was great 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!

Workshop Details

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

Spring 2024 Dates

May 28, and 30
9:00 AM – 11:00 AM