Bioinformatics: Single Cell RNA-Seq Workshop @ UC Davis

Dec. 18, 2017, 9:30 a.m. - Dec. 20, 2017, 4:30 p.m.

Organizer -

Bioinformatics Core

Contact -

UC Davis Bioinformatics Core,

This workshop will cover experimental design, data generation, and analysis of single cell RNA sequencing data (primarily generated using the 10x platform) on the command line and within the R statistical programming language. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services. Exercises will be performed on the command line and within R with a provided dataset. The primary packages used for analysis will be 10x software (for sequence reads to counts) and the R package Seurat for downstream analysis. The final half day will include a seminar and analysis presentation by 10X Genomics (


Monday VERY brief introduction to the command line and job submission to cluster resources. 
  Turning raw sequence data into counts data
Tuesday VERY brief Introduction to R
  The R package Seurat for single-cell data analysis
  Preparation, visualization and clustering of single cell data
Wednesday         Downstream analysis of data, differential expression, GO/KEGG analysis of clusters, marker identification
  10X Genomics Single-Cell Analysis


Lecture topics throughout the week will include:

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … There are no prerequisites other than familiarity with general biological concepts and an enthusiasm for learning bioinformatics data analysis. Some familiarity with the command-line and R is desirable.  However, we will dedicate some limited time to bringing everyone up-to-speed to be able to run the commands needed during this workshop.

What do I need to bring? … This workshop will be held in a computer room on the UC Davis campus, which has desktop computers running Microsoft Windows OS.  However, if you wish to bring your own laptop to use, it should have a recent version of Java installed, and an application that will allow you to ssh into a server (e.g. Putty for windows, or iTerm for Apple) as well as the ability to connect to the internet via wifi. Computational exercises will be performed on a remote server. If your department does not allow you to install software on the laptop you’ll be bringing, please contact us ahead of time.

Can I bring my own data? … We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How much does it cost? … The registration fee is $500 for UC and UC affiliates, $750 for other academic or non-profit participants and $1,500 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.  Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Where is the workshop? … It will be held in Davis and will run from 9:30am to 4:30pm on the dates indicated. The specific location will be provided at a later date.

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible to ensure your place in the workshop.

Where can I find more information, including your policies?  ... Go to our website ( and check out our FAQ and Policies.


If you have any questions, please don’t hesitate to contact us at

Registration is closed for this event