schedule.md

2019 Philadelphia CCDL Training

Location: 1429 Walnut St. Floor 10 Philadelphia, PA 19102

Dates: 10/14/2019 - 10/16/2019

Time	Topic
Day 1
9:00 AM	Welcome
9:10	Getting Started: Install Docker, Get files from flash drives, Docker container set up
10:00	Break
10:15	Introduction to R
11:00	R Intermediate Topics (including Tidyverse)
11:45	Exercises Introduction: Intro to R, Intro to Tidyverse
12:30	Lunch
1:30 PM	Bulk RNA-seq I: QC, trim, and quantification with Salmon
2:00	Bulk RNA-seq II: Gene-Level Summaries with tximport
2:45	Break
3:00	Bulk RNA-seq III: Exploratory Analyses
3:15	Bulk RNA-seq IV: Differential Expression Analysis: tximport, Differential Expression
4:45	Exercise Introduction: Bulk RNA-seq
5:00	End
Day 2
9:00 AM	scRNA-seq I: Normalizing a count matrix
10:15	Break
10:30	scRNA-seq II: Processing 10X data from raw
12:30 PM	Lunch
2:00	scRNA-seq III: Dimensionality reduction
2:45	Exercise Introduction: scRNA-seq
3:00	Break
3:30	Machine Learning: Data Preparation, Clustering, PLIER, Differential PLIER LVs
4:45	Exercise Introduction: Machine Learning
5:00	End
6:00	Dinner: Nomad Roman
Day 3
9:00 AM	Analyze your own data (or some stuff we have)!
12:30 PM	Lunch
2:00	Presentations, interpretations, and discussion
3:30	Break
4:00	Talk from CCDL data science team and wrap-up
5:00	Adjourn