diff --git a/workshop/SCHEDULE.md b/workshop/SCHEDULE.md index 5d381cd..d14538c 100644 --- a/workshop/SCHEDULE.md +++ b/workshop/SCHEDULE.md @@ -13,9 +13,9 @@ The planned schedule for the June 2024 Data Lab Virtual Training Workshop "Intro |-------------|--------------------------------------------|----------------| | **Day 1** | **2024-06-10**
_**Introduction to R and the Tidyverse**_ | | 12:00 PM | Welcome, Introductions and Getting Started
[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)
[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) | +| 1:00 PM | [Introduction to base R](../completed-notebooks/intro-to-R-tidyverse/01-intro_to_base_R.nb.html)
[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/intro-to-R-tidyverse/02-intro_to_ggplot2.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md) | +| 3:30 PM | [Introduction to the `tidyverse`](../completed-notebooks/intro-to-R-tidyverse/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) | | @@ -26,24 +26,24 @@ The planned schedule for the June 2024 Data Lab Virtual Training Workshop "Intro | | | | | **Day 2** | **2024-06-11**
_**Introduction to Single-cell RNA-seq, Day 1**_ | | 12:00 PM | Introduction
[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) | +| 12:30 PM | [scRNA-seq quantification with Alevin](../completed-notebooks/scRNA-seq/01-scRNA_quant_qc.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md)| +| 1:30 PM | [Importing data and filtering cells](../completed-notebooks/scRNA-seq/02-filtering_scRNA.nb.html) | Zoom: [Main Session](../software-setup/zoom-procedures.md) | +| 2:30 PM | [Normalization of expression data](../completed-notebooks/scRNA-seq/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**
_**Introduction to Single-cell RNA-seq, Day 2**_ | -| 12:00 PM | [Dimension reduction & visualization](#../completed-notebooks/04-dimension_reduction_scRNA.nb.html)
[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) | +| 12:00 PM | [Dimension reduction & visualization](../completed-notebooks/scRNA-seq/04-dimension_reduction_scRNA.nb.html)
[Dimension reduction and clustering slides (PDF)](#STUB) | Zoom: [Main Session](../software-setup/zoom-procedures.md)| +| 1:30 PM | [Clustering and marker identification](../completed-notebooks/scRNA-seq/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**
_**Introduction to Single-cell RNA-seq, Day 3**_ | | -| 12:00 PM | [Cell type annotation](#../completed-notebooks/06-celltype_annotation.nb.html)
[Cell type annotation slides (PDF)](#STUB) | Zoom: [Main Session](../software-setup/zoom-procedures.md) | +| 12:00 PM | [Cell type annotation](../completed-notebooks/scRNA-seq/06-celltype_annotation.nb.html)
[Cell type annotation slides (PDF)](#STUB) | 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) | |