Schedule
The CRI Bioinformatics Bootcamp will take place Saturday, May 17, 2025 through Thursday, May 22, 2025 at Wyndham Grand Bonnet Creek in Orlando, Florida.
| Day | Time | Duration | Module | Topic |
|---|---|---|---|---|
| 1 (Sat) | 9:00AM-9:30AM | 0:30 | R Workshop | Introduction to R and RStudio |
| 9:30AM-12:00PM | 2:30 | Hands-on: Reading, writing, and interpreting data structures | ||
| 12:00PM-1:30PM | 1:30 | Office Hours | Lunch | |
| 1:30PM-2:15PM | 0:45 | Introduction to plotting and statistics | ||
| 2:15PM-3:15PM | 1:00 | Hands-on: Plotting information from data structures for real-time analysis | ||
| 3:15PM-3:30PM | 0:15 | Break | ||
| 3:30PM-5:00PM | 1:30 | Hands-on (cont’d): Plotting | ||
| 2 (Sun) | 9:00AM-9:30AM | 0:30 | R Workshop | Types of analysis: Clustering concepts and correlation |
| 9:45AM-12:00PM | 2:30 | Hands-on: Dimension reduction methods, computing correlation | ||
| 12:00PM-1:30PM | 1:30 | Office Hours | Lunch | |
| 1:30PM-2:15PM | 0:45 | Common challenges and resources | ||
| 2:15PM-3:15PM | 1:00 | Hands-on: Creating different types of plots, continued practice | ||
| 3:15PM-3:30PM | 0:15 | Break | ||
| 3:30PM-5:00PM | 1:30 | Hands-on (cont’d): Continued practice | ||
| 3 (Mon) | 9:00AM-9:45AM | 0:45 | Bulk RNA sequencing | Introduction to sequencing data processing and analysis |
| 9:45AM-10:15AM | 0:30 | Introduction to rnabio.org | ||
| 10:15AM-10:30AM | 0:15 | Introduction to bulk RNAseq dataset | ||
| 10:30AM-11:30AM | 1:00 | Hands-on: Exploring RNAseq data in IGV | ||
| 11:30AM-12:00PM | 0:30 | Hands-on: DE analysis with DESeq2 | ||
| 12:00PM-1:30PM | 1:30 | Office Hours | Lunch | |
| 1:30PM-2:15PM | 0:45 | Hands-on: DE visualization with DESeq2 | ||
| 2:15PM-3:15PM | 1:00 | Hands-on: DE visualization advanced | ||
| 3:15PM-4:45PM | 1:30 | Hands-on: Pathway analysis | ||
| 4:45PM-5:00PM | 0:15 | Day 3 Summary/Questions | ||
| 5:30PM-7:00PM | 1:30 | Office Hours | ||
| 4 (Tue) | 9:00AM-9:45AM | 0:45 | Single cell RNA sequencing | Introduction to scRNAseq methods and analysis |
| 9:45AM-10:15AM | 0:30 | Introduction to scRNAseq dataset and loupe demonstration | ||
| 10:15AM-12:00PM | 1:45 | Hands-on: Quality assesment and clustering | ||
| 12:00PM-1:30PM | 1:30 | Office Hours | Lunch | |
| 1:30PM-2:15PM | 0:45 | Hands-on: Cell typing | ||
| 2:15PM-3:30PM | 1:15 | 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 | ||
| 5:30PM-7:00PM | 1:30 | Office hours | ||
| 5 (Wed) | 9:00AM-9:45AM | 0:45 | Single cell RNA sequencing | Advanced analyses in scRNAseq and multi-omic integration |
| 9:45AM-12:00PM | 2:00 | Hands-on: Cancer cell identification | ||
| 12:00PM-1:30PM | 1:30 | Office Hours | Lunch | |
| 1:30PM-3:00PM | 1:30 | Hands-on: Trajectory analysis | ||
| 3:00PM-4:15PM | 1:15 | Hands-on: TCR/BCR analysis | ||
| 4:15PM-4:45PM | 0:30 | vLoupe Browser demonstration | ||
| 4:45PM-5:00PM | 0:15 | Day 5 Summary/Questions | ||
| 6 (Thu) | 9:00AM-10:00AM | 1:00 | Spatial Transcriptomics | Introduction to spatial transcriptomics: Visium, Xenium, CosMx |
| 10:00AM-10:30AM | 0:30 | Sample pre-processing | ||
| 10:30AM-11:30PM | 1:00 | Seurat objects, motifs and neighborhood clustering (Banksy, Grafiti) | ||
| 11:30AM-12:00PM | 0:30 | Custom binning | ||
| 12:00PM-1:30PM | 1:30 | Office Hours | Lunch | |
| 1:30PM-2:30PM | 1:00 | Cell typing, CNV, trajectory analysis | ||
| 2:30PM-4:30PM | 2:00 | Hands-on: Unsupervised clustering, cell typing, loupe browser | ||
| 4:30PM-4:45PM | 0:15 | Day 6 Summary/Questions | ||
| 3:45PM-4:00PM | 0:15 | Conclusion | Closing and feedback |