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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

Quick Introduction to the Workshop and Core

The mission of the Bioinformatics Core facility is to facilitate outstanding omics-scale research through these activities:


Staff and Students

Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when appropriate, and/or develop novel applications and pipelines when needed, however we always emphasize biological interpretation of the data.



Workshop Goals


This workshop focuses on velocity and trajectory analysis. For differential expression analysis, consider Single Cell RNA-Seq Analysis.

Structure of the Virtual Workshops

Given the current Covid19 pandemic, and stay in place orders around the world, we’ve decided to take our popular bioinformatic workshops virtual. Our intent is to offer as close to an experience we can to our in-person workshops. We will hold the same goals and strive for a similar lecture/hand-on ratio. We will be using multiple technologies in order to help facilitate a maximum amount of interaction.


Course lecture, discussions, and one-on-one help/troubleshooting will be conducted using a zoom meeting.

Because video is involved, we ask everyone to be respectful and we reserve the right to remove someone if they are being disrespectful or disruptive.

Learn more about how we use Zoom in our workshops.


Text based communication will be conducted via a Slack channel. Staff will be monitoring the Slack channel to answer questions (and schedule a Zoom break out room if needed). If you know the answer to someone else’s question, feel free to answer it.

Learn more about how we use Slack in our workshops.

Workshop Materials

Workshop materials are all posted on github, and publicly available


Computing Cluster

A portion of this course will be conducted on our servers and compute cluster (tadpole.genomecenter.ucdavis.edu).

Instructions on how to get an account will be sent by email.