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Merge pull request #13 from AlexsLemonade/sjspielman/5-draft-schedule
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sjspielman authored Dec 3, 2024
2 parents 821780c + 6f1573e commit 21d851b
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1 change: 1 addition & 0 deletions components/dictionary.txt
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Expand Up @@ -24,6 +24,7 @@ cheatsheet
cheatsheets
checkmarks
compositional
contactless
COVID
customizable
Cynwyd
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1 change: 0 additions & 1 deletion workshop/HOME.md
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Expand Up @@ -18,7 +18,6 @@ Dates: {{site.start_date}} through {{site.end_date}}
### Pre-workshop Prep

* Please review the [Code of Conduct](../code-of-conduct.md).
* If you are new to using R, we've [assembled some resources for getting starting with R](../additional-resources/R-resources.md#pre-workshop-prep-for-r-programming) that can optionally help prepare you for the workshop.
* Please review the **[software platforms](../software-setup/software-setup-instructions.md)** we will be using to familiarize yourself with our procedures.
* You will also need to install
{%- case site.workshop_type -%}
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65 changes: 52 additions & 13 deletions workshop/SCHEDULE.md
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@@ -1,19 +1,58 @@
---
title: Workshop Schedule
title: Advanced scRNA-seq 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 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** | **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 |
4 changes: 2 additions & 2 deletions workshop/local-participant-information.md
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Expand Up @@ -29,14 +29,14 @@ If you have trouble finding the building or the room on the first day of trainin
**Public transportation**

* SEPTA is the public transportation system in Philadelphia and the surrounding area.
* At the airport, and at some SEPTA train stations, you can purchase a SEPTA key card. There are a variety of fare options that can be loaded onto a key card for use on public transportation. SEPTA also accepts cash for travel on any of its transit services.
* You can use cash or contactless pay (credit/debit card or Apple/Google/Samsung Pay) on SEPTA subways and buses.
* Please refer to the [SEPTA website](https://www5.septa.org/travel/) for more information. (**Note:** The [SEPTA trip planner](https://beta-plan.septa.org/#/) may be a helpful tool if you plan to travel around the city during your stay.)

#### Nearby Lodging

These hotels are within walking distance, or are a short Uber or Lyft ride, to One Bala Plaza.

ALSF receives a discounted rate at the **Courtyard by Marriott Philadelphia City Avenue**.
ALSF receives a discounted rate at the **Courtyard by Marriott Philadelphia City Avenue**.
[Use this link to book a reservation](https://www.marriott.com/event-reservations/reservation-link.mi?id=1687786457883&key=CORP&app=resvlink) at the discounted rate.

More hotels located within 1 mile of the workshop:
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