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      Introduction to 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
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
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

Tentative Virtual Schedule

Day 1

8:50 am Zoom session starts
9:00 am Welcome, format and expectations
9:30 am Connections logging in, environment, introductions
10:15 am 15 minute break
10:30 am Intro to the command line
10:45 am Hands on
11:00am Check in, more command line
11:15 am Hands on
11:30 am Check in, more command line
11:45 am Hands on
12:00 pm Lunch hour
1:00 pm Running jobs on a cluster
1:30 pm Hands on
1:45 pm Genomics/Bioinformatics Talk
2:45 pm 15 minute break
3:00 pm data reduction
3.45 pm 5 minute break
4:15 pm Hands on
4:45 pm Recap and Homework
5:00 pm Zoom session ends

Day 2

8:50 am Zoom session starts
9:00 am Recap and check everyones R session
9:15 am Introduction to R and RStudio
9:30 am Hands on
9:45 am Introduction to R and RStudio
10:00 am Hands on
10:20 am Wrap up Intro 2 R
10:30 am 15 minute break
10:45 am Experimental Design
11:25 am 5 minute break
12:00 pm Lunch hour
1:00 pm Wrap up Intro 2 R
2:00 pm Seurat Part 1
3:00 pm 15 minute break
3:15 pm Seurat Part 2
5:00 pm Zoom session ends

5:00pm - 6:00pm Happy hour discussion

Day 3

8:50 am Zoom session starts
9:00 am Recap and check everyones R session
9:30 am Seurat Part 3
10:30 am 15 minute break
11:30 am Cell Preparation by Diana Burkard-Waco
12:00 pm Lunch hour
1:00 pm Seurat part 4
2:00 pm Seurat part 5
3:00 pm 15 minute break
1:00 pm Seurat part 6
4:30 pm Closing
5:00 pm Zoom session ends