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Draft schedule #12

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merged 5 commits into from
May 23, 2024
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Draft schedule #12

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11dc39e
add draft schedule
sjspielman May 22, 2024
af8d043
completed notebooks instead
sjspielman May 22, 2024
ffee139
Merge branch 'main' into sjspielman/5-draft-schedule
sjspielman May 23, 2024
e3c12ce
Update workshop/SCHEDULE.md
sjspielman May 23, 2024
c161625
stubify the links
sjspielman May 23, 2024
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60 changes: 48 additions & 12 deletions workshop/SCHEDULE.md
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Expand Up @@ -3,17 +3,53 @@ title: Workshop Schedule
nav_title: Schedule
---

<!--See an example from a past remote workshop here: https://github.com/AlexsLemonade/2023-may-training/blob/main/workshop/SCHEDULE.md -->
<!--See an example from a past in-person workshop here: https://github.com/AlexsLemonade/2023-june-training/blob/main/workshop/SCHEDULE.md -->
The planned schedule for the June 2024 Data Lab Virtual Training Workshop "Introduction to Single-Cell RNA-Seq" appears below.


| Time | Topic |
|-------------|------------------------------------------------|
| **Day 1** | **Date** <br> <!--uncomment and add link: [Module]()--> |
| 12:00 PM | Welcome, Introductions and Getting Started <br>[Welcome Slides (PDF)](../slides/Workshop_Introduction.pdf)|
| 5:00 | End |
| **Day 2** | **Date** |
| **Day 3** | **Date** |
| **Day 4** | **Date** |
| **Day 5** | **Date** |
| 5:00 | Adjourn |
*Note: All times are [EDT (UTC−04:00)](https://www.timeanddate.com/time/zones/edt).*


| Time | Topic | Location |
|-------------|--------------------------------------------|----------------|
| **Day 1** | **2024-06-10** <br> _**Introduction to R and the Tidyverse**_ |
| 12:00 PM | Welcome, Introductions and Getting Started <br> [Workshop introduction slides (PDF)]() | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
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| 1:00 PM | [Introduction to base R](../completed-notebooks/01-intro_to_base_R.nb.html) <br> [Introduction to R, RStudio, and RStudio Server slides (PDF)]() | Zoom: [Main Session](../software-setup/zoom-procedures.md)|
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Since the notebook links are broken links at the moment, it probably doesn't make sense to have them here yet. We can add them as they are added to the repo.

| 2:30 PM | [Introduction to `ggplot2`](../completed-notebooks/02-intro_to_ggplot2.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 3:30 PM | [Introduction to the `tidyverse`](../completed-notebooks/03-intro_to_tidyverse.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 4:30 PM | Questions and introduction to the exercises | Zoom: [Breakout Rooms](../software-setup/zoom-procedures.md#using-breakout-rooms) |
| | [Exercise: Introduction to base R](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/intro-to-R-tidyverse/exercise_01-intro_to_base_R.Rmd) | |
| | [Exercise: Introduction to R](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/intro-to-R-tidyverse/exercise_02-intro_to_R.Rmd) | |
| | [Exercise: Introduction to the `tidyverse`, Part 1](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/intro-to-R-tidyverse/exercise_03a-intro_to_tidyverse.Rmd) | |
| | [Exercise: Introduction to the `tidyverse`, Part 2](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/intro-to-R-tidyverse/exercise_03b-intro_to_tidyverse.Rmd) | |
| | Exercises and [consultation sessions](workshop-logistics.md#consultation-sessions) | [Slack channel](../software-setup/slack-procedures.md) |
| 5:00 PM | *Adjourn for the day* |
| | | |
| **Day 2** | **2024-06-11** <br> _**Introduction to Single-cell RNA-seq, Day 1**_ |
| 12:00 PM | Introduction <br> [Introduction to scRNA-seq slides (PDF)]() | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 12:30 PM | [scRNA-seq quantification with Alevin](../completed-notebooks/01-scRNA_quant_qc.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md)|
| 1:30 PM | [Importing data and filtering cells](../completed-notebooks/02-filtering_scRNA.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 2:30 PM | [Normalization of expression data](../completed-notebooks/03-normalizing_scRNA.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 3:30 PM | Questions and introduction to the exercise | Zoom: [Breakout Rooms](../software-setup/zoom-procedures.md#using-breakout-rooms) |
| | [Exercise: scRNA-seq quantification](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq/exercise_01-scrna_quant.Rmd) | |
| | Exercises and [consultation sessions](workshop-logistics.md#consultation-sessions) | [Slack channel](../software-setup/slack-procedures.md) |
| 5:00 PM | *Adjourn for the day* |
| | | |
| **Day 3** | **2024-06-12** <br> _**Introduction to Single-cell RNA-seq, Day 2**_ |
| 12:00 PM | [Dimension reduction & visualization](../completed-notebooks/04-dimension_reduction_scRNA.nb.html) <br> [Dimension reduction and clustering slides (PDF)]() | Zoom: [Main Session](../software-setup/zoom-procedures.md)|
| 1:30 PM | [Clustering and marker identification](../completed-notebooks/05-clustering_markers_scRNA.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 3:00 PM | Questions and introduction to the exercise | Zoom: [Breakout Rooms](../software-setup/zoom-procedures.md#using-breakout-rooms) |
| | [Exercise: scRNA-seq clustering](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq/exercise_02-scrna_clustering.Rmd) | |
| | Exercises and [consultation sessions](workshop-logistics.md#consultation-sessions) | [Slack channel](../software-setup/slack-procedures.md) |
| 5:00 PM | *Adjourn for the day* |
| | | |
| **Day 4** | **2024-06-13** <br> _**Introduction to Single-cell RNA-seq, Day 3**_ | |
| 12:00 PM | [Cell type annotation](../completed-notebooks/06-celltype_annotation.nb.html) <br> [Cell type annotation slides (PDF)]() | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 2:30 PM | Questions and introduction to the exercise | Zoom: [Breakout Rooms](../software-setup/zoom-procedures.md#using-breakout-rooms) |
| | Exercises and [consultation sessions](workshop-logistics.md#consultation-sessions) | [Slack channel](../software-setup/slack-procedures.md)|
| | [Exercise: scRNA-seq cell type annotation](https://github.com/AlexsLemonade/training-modules/blob/{{site.release_tag}}/scRNA-seq/exercise_03-celltype.Rmd) | |
| 5:00 PM | *Adjourn for the day* |
| | |
| **Day 5** | **2024-06-14** <br> _**Consultation and Presentations**_ |
| 12:00 PM | [Consultation sessions](workshop-logistics.md#consultation-sessions) | [Slack channel](../software-setup/slack-procedures.md) |
| 2:30 PM | [Participant presentations begin](workshop-logistics.md#participant-presentations) | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 5:00 PM | *Adjourn* |
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