All documentation for the workshop is best viewed from the github.io pages
August 28 - 30, Wednesday, Thursday, 9 am to 3 pm, and Friday, 9 am to Noon.
Contact - UCSF CAT Bioinformatics , catbioinformatics@ucsf.edu
Workshop Description:
This 2.5-day in-person workshop includes a half-day of introductory material, followed by two days of focused, in-depth coursework on 10x single-cell RNA-seq. Participants will explore experimental design, data generation, data reduction, and basic analysis of single-cell RNA sequencing data using the command line and the R statistical programming environment. The course will cover software and protocols, workflow creation and modification, and diagnosing/treating problematic data using the command line and R code using Seurat. A basic understanding of the command line and R is highly recommended for success in this course. We will conduct a very brief review on the first morning, but we will not be providing full instruction in basic CLI or R.
Structure:
- Day 1 (Morning): Introductory Material
- Day 1 (Afternoon): Data reduction using 10X CellRanger and basic QA/QC
- Day 2 to Day 3 (Morning): In-depth R Coursework on scRNA-seq with Suerat.
- Sprinkled within will be talks and conversations, including experimental design, technology usage, and philosophy of analysis.
Focus Areas:
- Experimental Design
- Data Generation and Processing
- Data Analysis using the R package Seurat.
Learning Objectives:
- Conduct scRNA-Seq experiments using the command line and R.
- Create and modify Illumina 10X sequencing data processing workflows.
- Diagnose and address problematic data.
Prerequisites
Recommended: Basic understanding of the command line (CLI) and R. Intermediate Knowledge: Needed for maximum value from the course. Beginners: Can achieve a thorough understanding but may not be able to independently conduct an experiment.
Supplies Needed
A laptop with the command line terminal and R/Rstudio preinstalled.
Participants must have access to a computer with a reliable connection to the internet, current versions of R version 4.4.1, or at least R version >= 4.3.0 and Rstudio, and a terminal application.
We will have a dataset to use for the course, however you can bring your dataset for discussion purposes and feedback.
Recommendations for Beginners
Enroll in introductory courses in CLI and/or R courses to get the maximum out of the course.
Introductory Materials
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.