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      Fall single cell RNA sequencing workshop @ UCSF

Introduction and Lectures
Intro to the Workshop and Core
What is Bioinformatics/Genomics Perspective?
Experimental Design and Cost Estimation
Introduction to Command-Line and the Cluster
Logging in and Transferring Files
Intro to Command-Line
Advanced Command-Line (extra)
Running jobs on the Cluster and using modules
Intro to R and Rstudio
Getting Started
Intro to R
Prepare Data in R (extra)
Data in R (extra)
Data Reduction
Project setup
Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
scRNAseq Analysis - PART1
scRNAseq Analysis - PART2
scRNAseq Analysis - PART3
scRNAseq Analysis - PART4
scRNAseq Analysis - PART5
scRNAseq Analysis - PART6
Guest lecture by Dr. Gerald Quon
Prepare Single Cell Alignment
Single Cell Alignment (scAlign)
Cheat Sheets
Software and Links
Closing thoughts
Workshop Photos
Biocore website

Bioinformatics: scRNA-Seq Workshop @ UC San Francisco Nov. 25, 2019, 9 a.m. - Nov. 27, 2019, 4:30 p.m.
Organizer - UCD Bioinformatics Core
Contact - UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

This workshop will cover experimental design, data generation, and analysis of single cell RNA sequencing data (primarily generated using the 10x Genomics 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 cellranger (for sequence reads to counts) and R packages (ex. Seurat) for downstream analysis.

A preliminary agenda for the week includes:

Lecture topics throughout the week will include:

Industry Sponsors

Monday Celsee  
Tuesday Takara  
Wednesday 10x genomics  


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? … You will need to bring your own laptop to use, have a recent version of Java installed, and an application that will allow you to ssh into a server (e.g. Bash for windows 10, or terminal for Apple) as well as the ability to connect to the internet via wifi. Computational exercises will be performed on a remote server. We can help with setup early on in the workshop. 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.

Where is the workshop? … It will be held in Genentech Hall at UCSF and will run from 9:30am to 4:30pm on the dates indicated. The room number 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 (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.


If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu



Registration is closed for this event