Merge pull request #20 from AlexsLemonade/sjspielman/9-final-schedule

Finalize slides and schedule
AlexsLemonade · Dec 5, 2024 · b154c45 · b154c45
2 parents 8ab6d7c + 8414528
commit b154c45
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 11 deletions.
diff --git a/slides/2024-12-10_welcome-introduction.pdf b/slides/2024-12-10_welcome-introduction.pdf
diff --git a/workshop/SCHEDULE.md b/workshop/SCHEDULE.md
@@ -6,32 +6,31 @@ 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
+| 9:00 AM   | [Welcome, Introductions and Getting Started](../slides/2024-12-10_welcome-introduction.pdf)
 | 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
+|           | [Single-cell Analysis with R slides (PDF)](../slides/2024-12-10_scRNAseq-data-intro.pdf)
+|           | [Instruction notebook](../completed-notebooks/scRNA-seq-advanced/01-read_filter_normalize_scRNA.nb.html)
 | 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
 |           | [Integration slides (PDF)](../slides/2024-12-10_integration.pdf)
-|           | Instruction notebook
+|           | [Instruction notebook](../completed-notebooks/scRNA-seq-advanced/02-dataset_integration.nb.html)
 | 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
+|           | [Differential Expression slides (PDF)](../slides/2024-12-11_differential-expression.pdf)
+|           | [Instruction notebook](../completed-notebooks/scRNA-seq-advanced/03-differential_expression.nb.html)
 | 11:00 AM  | *Coffee break*
 | 11:15 AM  | Differential Expression Analysis, continued
 | 12:30 PM  | *Lunch*
@@ -45,12 +44,13 @@ The planned schedule for the December 10-12, 2024 Data Lab Training Workshop app
 | 9:00 AM   | Questions and Review
 | 9:30 AM   | Pathway Analysis
 |           | [Pathway Analysis Slides (PDF)](../slides/2024-12-12_pathway-analysis.pdf)
-|           | Instruction notebook: Gene-set enrichment analysis (GSEA)
+|           | [Instruction notebook: Gene Set Enrichment Analysis (GSEA)](../completed-notebooks/scRNA-seq-advanced/04-gene_set_enrichment_analysis.nb.html)
 | 11:00 AM  | *Coffee break*
-| 11:15 AM  | Instruction notebook: AUCell
+| 11:15 AM  | [Instruction notebook: AUCell](../completed-notebooks/scRNA-seq-advanced/05-aucell.nb.html)
 | 12:30 PM  | *Lunch*
 | 1:30 PM   | Exercises, Questions, and Independent Projects
-|           | Exercise: AUCell
+|           | [Exercise: AUCell](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_04-scrna_pathway.Rmd)
+|           | [Exercise: Evaluating cluster quality](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq-advanced/exercise_05-cluster_evaluation.Rmd)
 |           | [Resources for consultation sessions](./workshop-resources.md)
 | 3:00 PM   | Participant Presentations!
 | 4:00 PM   | *Adjourn*