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      Introduction to Single Cell RNA-Seq Workshop

Introduction and Lectures
Intro to the Workshop and Core
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
Single Cell Sample Preparation - Dr. Diana Burkart-Waco
Biology at True Resolution - Introduction to Single Cell and Visium Spatial Solutions
Visium Spatial Protocols - Tissue Preparation Guide
Using Slack in this workshop
Using Zoom in this workshop
Cheat Sheets
Software and Links
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (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
Shiny App (extra)
Shiny App on AWS (extra)
Closing thoughts
Workshop Photos
Github page
Biocore website

All documentation for the workshop is best viewed from the github.io pages


Bioinformatics: Introduction to Single Cell RNA-Seq Analysis Workshop

Aug. 12, 2020 - Aug. 14, 2020, 9 a.m. - 4:30 p.m daily. Online learning

Contact - UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

This workshop will cover experimental design, data generation, data reduction and basic analysis of single cell RNA sequencing data (Example dataset is from the 10x Genomics platform) on the ‘command line’ and within the R statistical programming environment. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services and R code. Within this introductory course we will use 10x Genonics software cellranger for data reduction (sequence reads to counts) and R packages (ex. Seurat) for downstream analysis.

There are no prerequisites other than basic familiarity with genomic concepts. Anyone with an interest in scRNA sequence analysis is welcome! Some familiarity with the command-line and R is helpful. However, we will dedicate some small amount of time to bringing everyone up-to-speed to be able to run the commands needed during this workshop. This workshop will be held online via Zoom and will run from 9:00am to 5:00pm each day with an hour break for lunch.

Participants must supply their own laptop/desktop with a reliable connection to the internet. The labtop/desktop should have a current versions of R version 4.0, Rstudio, and Java installed, and an application that allows them to ssh into a server (e.g. Bash for Windows, or Terminal for Apple)


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 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, and an application that will allow you to ssh into a server (e.g. Bash for windows, or terminal for Apple OSX). 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 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 $1,500 for current students, postdocs, staff and faculty at Univeristy of California campus’ or UC National Labs (LBNL, LANL, LLNL), $1,750 for other academic or non-profit participants and $2,500 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.

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


Register for the August 2020 online course