2020 CCDL Virtual Training @ Pittsburgh

Traning material developed by Childhood Cancer Data Lab
Alex’s Lemonade Stand Foundation https://www.alexslemonade.org

Training adapted and delivered by Huajin Wang and Christina Akirtava, Carnegie Mellon University, as part of the Data Collaborations Lab at CMU Libraries

Location: Virtually by Zoom

Dates: 08/17/2020 - 08/21/2020

Schedule

Note: All times are EDT (UTC−04:00)

Time Topic Location
Day 1 2020-08-17
Introduction to R and the Tidyverse		  
12:00 Welcome, Introductions and Getting Started
Workshop Intro Slides (pdf)		 Zoom: Main Session
1:00 Introduction to base R
Intro to RStudio Slides (pdf)		 Zoom: Main Session
3:00 Questions and introduction to the exercise:
Introduction to R Exercise		 Zoom: Breakout Rooms
3:30 Consultation session begins #2020-pgh-training Slack channel
5:00 End  
Day 2 2020-08-18
Introduction to R and the Tidyverse		  
12:00 Introduction to ggplot2 Zoom: Main Session
  Introduction to the Tidyverse Zoom: Main Session
3:00 Questions and introduction to the exercises:
Introduction to R Exercise
Introduction to the Tidyverse Exercise - Part 1
Introduction to the Tidyverse Exercise - Part 2		 Zoom: Breakout Rooms
3:30 Consultation session begins #2020-pgh-training Slack channel
5:00 End  
Day 3 2020-08-19
Introduction to Bulk RNA-seq		  
12:00 Bulk RNA-seq I: QC, trim, and quantification with Salmon
Intro to Bulk RNA-seq Slides (pdf)		 Zoom: Main Session
1:30 Bulk RNA-seq II: Gene-Level Summaries with tximport Zoom: Main Session
2:30 Bulk RNA-seq III: Exploratory Analyses Zoom: Main Session
3:00 Questions and introduction to the exercise:
Exploratory Data Analysis		 Zoom: Breakout Rooms
3:30 Consultation session begins #2020-pgh-training Slack channel
5:00 End  
Day 4 2020-08-20
Introduction to Bulk RNA-seq		  
12:00 Guided Exercise: Neuroblastoma Cell Line tximport Zoom: Breakout Rooms (meet in main session to begin)
1:30 Bulk RNA-seq IV: Differential Expression Analysis Zoom: Main Session
3:00 Questions and introduction to the exercise:
Bulk RNA-seq Exercise		 Zoom: Breakout Rooms
3:30 Consultation session begins #2020-pgh-training Slack channel
5:00 End  
Day 5 2020-08-21
Consultation and Presentations		  
12:00 Consultation session begins #2020-pgh-training Slack channel
1:30 Presentations begin Zoom: Main Session
4:00 Adjourn