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      Single Cell RNA-Seq Analysis

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
Talk by Diana Burkhat-Waco from 10x Genomics
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
Support
Zoom
Slack
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI
R
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 Data Explore
Shiny App on AWS (extra)
ETC
Closing thoughts
Github page
Biocore website

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

Documentation

Single Cell RNA-Seq Analysis

Mar. 22, 2021 - Mar. 24, 2021, 9 a.m. - 5:00 p.m daily. Online learning

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

This three-day online workshop covers experimental design, data generation, and analysis of single cell RNA sequencing data. Participants will explore a single cell experiment using the command line and R, create and modify workflows, and diagnose and treat problematic data utilizing high performance computing services. The primary packages used for analysis will be 10x software for sequence reads to counts, and the R package Seurat for downstream analysis.

To get the most out of this course, please complete the prerequisite material in command line and R before the course, and contact us with any questions.

This workshop will be held online from 9:00 am to 5:00 pm each day.

Participants will need access to a computer with a reliable connection to the internet, a current versions of R version and Rstudio installed, and an application that allows them to ssh into a server (e.g. Bash for Windows, or Terminal for Apple).

This workshop is generously supported by 10x Genomics.

10x Genomics

FAQ

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … To get the most out of this course, please complete the prerequisite material in command line and R before the course, and contact us with any questions.

What do I need? … You will need access to a computer with a reliable connection to the internet, a current versions of R version and Rstudio installed, and an application that allows them to ssh into a server (e.g. Bash for Windows, or Terminal for Apple). If your department does not allow you to install software on your computer, 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.

Questions

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

Register

Register for Single Cell RNA-Seq at the Genome Center Event Registration site.