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      Adv Topics in scRNA-Seq: Trajectory and Velocity Analysis

Introduction and Lectures
Intro to the Workshop and Core
Using Slack in this workshop
Using Zoom in this workshop
Cheat Sheets
Software and Links
More Materials - Intro CLI
More Materials - Intro R
Velocity Analysis
Velocity data reduction
Prepare for Velocity analysis
Velocity data analysis
Monocle Trajectory Analysis
Prepare for Monocle
Closing thoughts
Github page
Biocore website

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


Aug. 13, 2021, 9 a.m. - 4:30 p.m. online learning

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

This workshop will cover trajectory and velocity analyses with single cell RNA sequencing data on the command line and within the R statistical programming language. Exercises will be performed on the command line and within R with a provided dataset.

Participants should be familiar with basic single cell RNA-Seq expression analysis, which will not be covered in this workshop.

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 or higher, Rstudio, and an application that allows them to ssh into a server.


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 access to a computer with a strong internet connection and an application that will allow you to ssh into a server (e.g. Bash for windows, or terminal for Apple OSX). If your department does not allow you to install software on the computer you’ll be using, 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 $500 for current students, postdocs, staff and faculty at Univeristy of California campus’ or UC National Labs (LBNL, LANL, LLNL), $700 for other academic or non-profit participants and $1,000 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 and check out our FAQ and Policies.


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