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      Advanced Single Cell RNA-Seq Workshop

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
Single Cell Sample Preparation - Dr. Diana Burkart-Waco
Support
Cheat Sheets
Software and Links
Scripts
Prerequisites
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
Generating Expression Matrices
Expression project setup
Preprocessing reads with HTStream
Generating Expression Tables
VDJ T cell and B cell
Velocity analysis
Data analysis
scRNA analysis prepare
Mapping Comparison
Anchoring (Comparison dataset)
Shiny App Install/Overview
App Practical Usage
AWS Hosted App (Optional)
Monocle
VDJ T cell and B cell analysis
Velocity analysis
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

Closing Thoughts

The forest through the trees.

flowchart2

Be Consistent

Prerequisites for bioinformatics

The bottom line

Next Steps

My recommendation is to follow all of the instructions again, from the beginning on your own and send emails to training.bioinformatics@ucdavis.edu And we will be responsive to answering questions

Upcoming Workshops

Now in our 13th year of training researchers, the UC Davis Bioinformatics Core invites you to attend one or more of our 2020 workshops. The following workshops are suitable for beginners to advanced researchers, and are also of interest to those with some data analysis experience.

Jun 1 - Jun 4, 2020 Remote RNA-Seq Workshop
Jun 29 - Jul 2, 2020 Remote Genome Assembly
Jul 27 - Jul 31, 2020 RNA-Seq Workshop @ UC Davis
Aug 12 - Aug 14, 2020 Introduction to Single Cell RNA-Seq @ UC Davis
Aug 17 - Aug 19, 2020 Advanced Single Cell RNA-Seq @ UC Davis
Oct 5 - Oct 9, 2020 Bioinformatics: Command Line/R Prerequisites
Nov 30 - Dec 4, 2020 Introduction to Analysis of Epigenetic Data

For more information on these and other events, and to register, go to https://registration.genomecenter.ucdavis.edu/

Previous Workshops available online

If you would like to take a look at the documentation from previous workshops.

Questions?

Contact us at training.bioinformatics@ucdavis.edu

If you receive email directly from training.bioinformatics@ucdavis.edu, you are currently subscribed to one of our announcements lists. To subscribe / unsubscribe from the Bioinformatics Core email lists, please follow the instructions at the bottom of http://bioinformatics.ucdavis.edu/contact-us/.