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sjspielman authored May 23, 2024
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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)](#STUB) | Zoom: [Main Session](../software-setup/zoom-procedures.md) |
| 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)](#STUB) | Zoom: [Main Session](../software-setup/zoom-procedures.md)|
| 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)](#STUB) | 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)](#STUB) | 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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