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Merge pull request #15 from AlexsLemonade/jashapiro/intro-diff-slides
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Add slides for scRNAseq intro & differential expression
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jashapiro authored Dec 4, 2024
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Expand Up @@ -5,54 +5,54 @@ nav_title: Schedule

The planned schedule for the December 10-12, 2024 Data Lab Training Workshop appears below.

| Time | Topic |
| --------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| **Day 1** | **2024-12-10** |
| 9:00 AM | Welcome, Introductions and Getting Started |
| 10:00 AM | Introduction/Refresher to Single-cell Analysis with R and Bioconductor |
| | Slides |
| | Instruction notebook |
| 11:15 AM | *Coffee break* |
| 11:30 AM | Introduction/Refresher to Single-cell Analysis, continued |
| 12:15 PM | *Lunch* |
| 1:15 PM | Integrating scRNA-seq Experiments |
| | Slides |
| | Instruction notebook |
| 2:30 PM | *Coffee break* |
| 2:45 PM | Integrating scRNA-seq Experiments, continued |
| 4:15 PM | Exercises and Questions |
| | [Exercise: Importing CITE-seq data](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_01-citeseq.Rmd) |
| | [Exercise: Cell type assignment](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq/exercise_03-celltype.Rmd) <br> _This exercise is available in the `scRNA-seq` module_ |
| | Exercise: Evaluating cluster quality |
| | [Exercise: Integration](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_02-integration.Rmd) |
| 5:00 PM | *Adjourn for the day* |
| | |
| **Day 2** | **2024-12-11** |
| 9:00 AM | Questions and Review |
| 9:30 AM | Differential Expression Analysis with scRNA-seq |
| | Slides |
| | Instruction notebook |
| 11:00 AM | *Coffee break* |
| 11:15 AM | Differential Expression Analysis, continued |
| 12:30 PM | *Lunch* |
| 1:30 PM | Exercises, Questions, and Independent Projects |
| | [Exercise: Differential Expression](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_03-diffexp.Rmd) |
| | [Resources for consultation sessions](./workshop-resources.md) |
| 4:00 PM | *Adjourn for the day* |
| 6:00 PM | Workshop dinner: [Couch Tomato](https://www.thetomatoshack.com/location/The-Couch-Tomato-Cafe-Manayunk/) <br> 102 Rector Street <br> Philadelphia, PA 19127 |
| | |
| **Day 3** | **2024-12-12** |
| 9:00 AM | Questions and Review |
| 9:30 AM | Pathway analysis |
| | Slides |
| | Instruction notebook: Gene-set enrichment analysis (GSEA) |
| 11:00 AM | *Coffee break* |
| 11:15 AM | GSEA, continued |
| 12:30 PM | *Lunch* |
| 1:30 PM | Exercises, Questions, and Independent Projects |
| | Exercise: GSEA |
| | [Resources for consultation sessions](./workshop-resources.md) |
| 3:00 PM | Participant Presentations! |
| 4:00 PM | *Adjourn* |
| Time | Topic
| --------- | -----------------------
| **Day 1** | **2024-12-10**
| 9:00 AM | Welcome, Introductions and Getting Started
| 10:00 AM | Introduction/Refresher to Single-cell Analysis with R and Bioconductor
| | [ Single-cell Analysis with R slides (PDF) ](../slides/2024-12-10_scRNAseq-data-intro.pdf)
| | Instruction notebook
| 11:15 AM | *Coffee break*
| 11:30 AM | Introduction/Refresher to Single-cell Analysis, continued
| 12:15 PM | *Lunch*
| 1:15 PM | Integrating scRNA-seq Experiments
| | Slides
| | Instruction notebook
| 2:30 PM | *Coffee break*
| 2:45 PM | Integrating scRNA-seq Experiments, continued
| 4:15 PM | Exercises and Questions
| | [Exercise: Importing CITE-seq data](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_01-citeseq.Rmd)
| | [Exercise: Cell type assignment](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq/exercise_03-celltype.Rmd) <br> _This exercise is available in the `scRNA-seq` module_
| | Exercise: Evaluating cluster quality
| | [Exercise: Integration](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_02-integration.Rmd)
| 5:00 PM | *Adjourn for the day*
| |
| **Day 2** | **2024-12-11**
| 9:00 AM | Questions and Review
| 9:30 AM | Differential Expression Analysis with scRNA-seq
| | [ Differential Expression slides (PDF) ](../slides/2024-12-11_differential-expression.pdf)
| | Instruction notebook
| 11:00 AM | *Coffee break*
| 11:15 AM | Differential Expression Analysis, continued
| 12:30 PM | *Lunch*
| 1:30 PM | Exercises, Questions, and Independent Projects
| | [Exercise: Differential Expression](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_03-diffexp.Rmd)
| | [Resources for consultation sessions](./workshop-resources.md)
| 4:00 PM | *Adjourn for the day*
| 6:00 PM | Workshop dinner: [Couch Tomato](https://www.thetomatoshack.com/location/The-Couch-Tomato-Cafe-Manayunk/) <br> 102 Rector Street <br> Philadelphia, PA 19127
| |
| **Day 3** | **2024-12-12**
| 9:00 AM | Questions and Review
| 9:30 AM | Pathway analysis
| | Slides
| | Instruction notebook: Gene-set enrichment analysis (GSEA)
| 11:00 AM | *Coffee break*
| 11:15 AM | GSEA, continued
| 12:30 PM | *Lunch*
| 1:30 PM | Exercises, Questions, and Independent Projects
| | Exercise: GSEA
| | [Resources for consultation sessions](./workshop-resources.md)
| 3:00 PM | Participant Presentations!
| 4:00 PM | *Adjourn*


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