Schedule

The inaugural CRI Bioinformatics Bootcamp will take place April 27, 2024-May 2, 2024 at the Hilton Bonnett Creek, Orlando FL.

Day	Time	Duration	Module	Topic
1 (Sat)	9:00AM-9:30AM	0:30	R Workshop	Introduction to R and RStudio
	9:30AM-9:45AM	0:15		Break
	9:45AM-12:00PM	2:15		Hands-on: Reading, writing, and interpreting data structures
	12:00PM-1:00PM	1:00		Lunch
	1:00PM-1:45PM	0:45		Introduction to plotting and statistics
	1:45PM-2:00PM	0:15		Break
	2:00PM-4:30PM	2:30		Hands-on: Plotting information from data structures for real-time analysis
2 (Sun)	9:00AM-9:30AM	0:30	R Workshop	Types of analysis: Clustering concepts and correlation
	9:30AM-9:45AM	0:15		Break
	9:45AM-12:00PM	2:15		Hands-on: Dimension reduction methods, computing correlation
	12:00PM-1:00PM	1:00		Lunch
	1:00PM-1:45PM	0:45		Common challenges and resources
	1:45PM-2:00PM	0:15		Break
	2:00PM-4:30PM	2:30		Hands-on: Creating different types of plots, continued practice
3 (Mon)	9:00AM-9:45AM	0:45	Bulk DNA/RNA sequencing	Introduction to sequencing data processing and analysis
	9:45AM-10:00AM	0:15		Break
	10:00AM-10:30AM	0:30		Introduction to rnabio.org
	10:30AM-10:45AM	0:15		Introduction to bulk RNAseq dataset
	10:45AM-11:30AM	0:45		Hands-on: Exploring RNAseq data in IGV
	11:30AM-12:00PM	0:30		Hands-on: DE analysis with DESeq2
	12:00PM-1:00PM	1:00		Lunch
	1:00PM-1:45PM	0:45		Hands-on: DE visualization with DESeq2
	1:45PM-2:00PM	0:15		Break
	2:00PM-3:00PM	1:00		Hands-on: DE visualization advanced
	3:00PM-4:00PM	1:00		Hands-on: Pathway analysis
	4:00PM-4:45PM	0:45		Hands-on: Batch correction
	4:45PM-5:00PM	0:15		Day 3 Summary/Questions
4 (Tue)	9:00AM-9:45AM	0:45	Single cell RNA sequencing	Introduction to scRNAseq methods and analysis
	9:45AM-10:00AM	0:15		Break
	10:00AM-10:30AM	0:30		Introduction to scRNAseq dataset and loupe demonstration
	10:45AM-12:00PM	1:15		Hands-on: Quality assesment and clustering
	12:00PM-1:00PM	1:00		Lunch
	1:00PM-1:45PM	0:45		Hands-on: Cell typing
	1:45PM-2:00PM	0:15		Break
	2:00PM-3:30PM	1:30		Hands-on: DE analysis
	3:30PM-4:45PM	1:15		Hands-on: Gene set and regulatory pathway
	4:45PM-5:00PM	0:15		Day 4 Summary/Questions
5 (Wed)	9:00AM-9:45AM	0:45	Single cell RNA sequencing	Advanced analyses in scRNAseq and multi-omic integration
	9:45AM-10:00AM	0:15		Break
	10:00AM-12:00PM	2:00		Hands-on: Cancer cell identification
	12:00PM-1:00PM	1:00		Lunch
	1:00PM-2:30PM	1:30		Hands-on: Trajectory analysis
	2:30PM-2:45PM	0:15		Break
	2:45PM-4:00PM	1:15		Hands-on: TCR/BCR analysis
	4:00PM-4:30PM	0:30		vLoupe Browser demonstration
	4:30PM-5:00PM	0:30		Day 5 Summary/Questions
6 (Thu)	9:00AM-9:45AM	0:45	Imaging	Overview of spatial biology, types of imaging, experimental planning
	10:00AM-10:30AM	0:30		Imaging file types, visualization platforms
	10:30AM-10:45AM	0:15		Break
	10:45AM-11:30PM	0:45		Hands-on: Exploring datasets
	11:30AM-12:00PM	0:30		Mini-lecture and hands-on: Introduction to python
	12:00PM-1:00PM	1:00		Lunch
	1:00PM-2:00PM	1:00		Quantifying spatial features from imaging data
	2:00PM-3:45PM	1:45		Hands-on: Spatial feature extraction
	3:45PM-4:00PM	0:15	Conclusion	Closing and feedback