UMGCCCFCSR · jttoivon · Feb 10, 2026 · Feb 12, 2026 · Feb 14, 2026 · Feb 14, 2026
diff --git a/Announcements.qmd b/Announcements.qmd
@@ -0,0 +1,43 @@
+---
+title: "Announcements"
+format: html
+toc: TRUE
+toc-location: right
+sidebar: false
+---
+
+![](/images/WebsiteBanner.png)
+
+For previous course announcements emails, see the links below. 
+
+- January 21, 2026 [Cytometry in R - Start Date, Livestream Times, Pre-Course Materials](https://github.com/UMGCCCFCSR/CytometryInR/discussions/7) 
+
+- February 01, 2026 [Cytometry In R - Week #1 - Installing R packages](https://github.com/UMGCCCFCSR/CytometryInR/discussions/11) 
+
+- February 09, 2026 [Cytometry in R - Week # 2 - File Paths](https://github.com/UMGCCCFCSR/CytometryInR/discussions/41) 
+
+- February 16, 2026 [Cytometry in R - Week #03 - Inside an FCS File](https://github.com/UMGCCCFCSR/CytometryInR/discussions/65) 
+
+- February 22, 2026 [Cytometry in R - Week #4 - Introduction to Tidyverse](https://github.com/UMGCCCFCSR/CytometryInR/discussions/85) 
+
+- March 01, 2026 [Cytometry in R - Week #5 - Gating Sets](https://github.com/UMGCCCFCSR/CytometryInR/discussions/103) 
+
+- March 10, 2026 [No Class This Week](https://github.com/UMGCCCFCSR/CytometryInR/discussions/128) 
+
+- March 17, 2026 [Cytometry in R - Week # 6 - Visualizing with ggplot2](https://github.com/UMGCCCFCSR/CytometryInR/discussions/132) 
+
+- March 24, 2026 [Cytometry in R - Week # 07 - Applying Transformations](https://github.com/UMGCCCFCSR/CytometryInR/discussions/145) 
+
+- March 30, 2026 [Cytometry in R - Course Feedback Survey #1](https://github.com/UMGCCCFCSR/CytometryInR/discussions/151) 
+
+- April 07, 2026 [Cytometry in R - Week # 08 - Manual and Automated Gating](https://github.com/UMGCCCFCSR/CytometryInR/discussions/159) 
+
+- April 12, 2026 [Cytometry in R - Week # 09 - It's Raining Functions!](https://github.com/UMGCCCFCSR/CytometryInR/discussions/162) 
+
+- April 21, 2026 [No Class This Week](https://github.com/UMGCCCFCSR/CytometryInR/discussions/174)
+
+- April 28, 2026 [Cytometry in R - Week # 10 - Downsampling and Concatenation](https://github.com/UMGCCCFCSR/CytometryInR/discussions/179)
+
+- May 05, 2026 [Cytometry in R - Week # 11 - Data for Statistics](https://github.com/UMGCCCFCSR/CytometryInR/discussions/186)
+
+![](images/YouTubeHex.png)
diff --git a/Homeworks.qmd b/Homeworks.qmd
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ Cytometry in R is a free virtual mini-course being organized by the [Flow Cytome
 
 We are excited that so many individuals worldwide have chosen to take part, and we look forward to helping you get started on your own learning journeys. 
 
-![](/images/WorldwideSignups.png){width=100%}
+![](/images/WorldwideSignups.png){width="100%"}
 
 Click here to go to our [Course Website](https://umgcccfcsr.github.io/CytometryInR)
 

diff --git a/Schedule.qmd b/Schedule.qmd
@@ -106,7 +106,7 @@ No class week of March 30, 2026. If you are attending the [ABRF conference](http
 
 ![](images/openCyto.png){width=75%}
 
-[**Week 8: April 6, 2026**]{.underline} Within this session, we explore various ways to implement gating for flow cytometry files in R. We will explore manual approaches utilizing [flowGate](https://www.bioconductor.org/packages/release/bioc/html/flowGate.html), as well as automated options with [openCyto](https://www.bioconductor.org/packages/release/bioc/vignettes/openCyto/inst/doc/HowToAutoGating.html) and it's gating templates. We additionally will explore how to provide gate constraints and various ways to visually screen and evaluate the outcomes within the context of our own projects.
+[**Week 8: April 6, 2026**]{.underline} Within this [eight](/course/08_WaysToGate/index.qmd) session, we explore various ways to implement gating for flow cytometry files in R. We will explore manual approaches utilizing [flowGate](https://www.bioconductor.org/packages/release/bioc/html/flowGate.html), as well as automated options with [openCyto](https://www.bioconductor.org/packages/release/bioc/vignettes/openCyto/inst/doc/HowToAutoGating.html) and it's gating templates. We additionally will explore how to provide gate constraints and various ways to visually screen and evaluate the outcomes within the context of our own projects.
 
 <br>
 <br>
@@ -117,7 +117,7 @@ No class week of March 30, 2026. If you are attending the [ABRF conference](http
 
 ![](https://images2.minutemediacdn.com/image/upload/c_fill,w_720,ar_16:9,f_auto,q_auto,g_auto/shape/cover/sport/raining-monkeys-e3fa8001e4eb47433b1cc58e2017d2b8.png){width=75%}
 
-[**Week 9: April 13, 2026**]{.underline} In the course of this ninth session, we tackle one of the harder but most useful concepts to learn for a beginner, namely [functions](https://r4ds.had.co.nz/functions.html). We explore what they are, how their individual arguments work, how they differ from for-loops, and how to create our own to do useful work, reduce the number times code gets copied and pasted. Additionally, some functional programming best practices will be introduced, as well as provide introduction to how to use the walk and map functions from the [purrr](https://purrr.tidyverse.org/) package. 
+[**Week 9: April 13, 2026**]{.underline} In the course of this [ninth](/course/09_Functions/index.qmd) session, we tackle one of the harder but most useful concepts to learn for a beginner, namely [functions](https://r4ds.had.co.nz/functions.html). We explore what they are, how their individual arguments work, how they differ from for-loops, and how to create our own to do useful work, reduce the number times code gets copied and pasted. Additionally, some functional programming best practices will be introduced, as well as provide introduction to how to use the walk and map functions from the [purrr](https://purrr.tidyverse.org/) package. 
 
 <br>
 <br>
@@ -126,7 +126,7 @@ No class week of March 30, 2026. If you are attending the [ABRF conference](http
 
 ![](https://www.ibm.com/content/dam/connectedassets-adobe-cms/worldwide-content/creative-assets/s-migr/ul/g/7d/10/downsampling-near-miss-v3.png){width=50%}
 
-[**Week 10: April 20, 2026**]{.underline} Within this session, we will expand on our growing understanding of GatingSets, functions and fcs file internals to write a script to downsample your fcs files to a desired number (or percentage) of cells for a given cell population. We will additionally learn how to concatenate these downsampled files together, and save them to a new .fcs file in ways that the metadata can be read by commercial software without the scaling being widely thrown off.  
+[**Week 10: April 20, 2026**]{.underline} Within this [tenth](/course/10_Downsampling/index.qmd) session, we will expand on our growing understanding of GatingSets, functions and fcs file internals to write a function to downsample your fcs files to a desired number (or percentage) of cells for a given cell population. We will additionally learn how to concatenate these downsampled files together, and save them to a new .fcs file in ways that the metadata can be read by commercial software without the scaling being widely thrown off.  
 
 <br>
 <br>
@@ -135,7 +135,7 @@ No class week of March 30, 2026. If you are attending the [ABRF conference](http
 
 ![](images/TidyData.png){width=33%}
 
-[**Week 11: April 27, 2026**]{.underline} Leveraging the increased familiarity working with the various packages this far in the course, in this session we will retrieve summary statistics for the gates within our GatingSet, and programmatically derrive out tidy data.frames for use in statistical analyses typically used by many Immunologist. In the process, we add a couple additional plot types to our ggplot2 arsenal to hold in reserve should Prism prices go up again. 
+[**Week 11: April 27, 2026**]{.underline} Leveraging the increased familiarity working with the various packages this far in the course, in this [eleventh](/course/11_DataForStats/index.qmd) session we will retrieve summary statistics for the gates within our GatingSet, and programmatically derrive out tidy data.frames for use in statistical analyses typically used by many Immunologist. In the process, we add a couple additional plot types to our ggplot2 arsenal to hold in reserve should Prism prices go up again. 
 
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diff --git a/_quarto.yml b/_quarto.yml
@@ -6,15 +6,23 @@ project:
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+    - Announcements.qmd
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+    - course/TakeAwayGallery.qmd
     - 00_*
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@@ -35,11 +43,15 @@ website:
         href: Schedule.qmd
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+      - text: "Announcements"
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     right:
     - text: Existing Resources
       href: ExistingResources.qmd
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       href: https://github.com/UMGCCCFCSR/CytometryInR/discussions
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@@ -82,12 +94,26 @@ website:
         href: course/06_Visualizing/index.qmd
       - text: "07 - Applying Transformations"
         href: course/07_Transformations/index.qmd
+      - text: "08 - Ways to Gate"
+        href: course/08_WaysToGate/index.qmd    
+      - text: "09 - It's Raining Functions!"
+        href: course/09_Functions/index.qmd 
     - section: "Cytometry Core"
-      href: Schedule.qmd
+      contents:
+      - text: "10 - Downsampling and Concatenation"
+        href: course/10_Downsampling/index.qmd
+      - text: "11 - Data for Statistics"
+        href: course/11_DataForStats/index.qmd
     - section: "Beyond the Sandbox"
       href: Schedule.qmd
     - section: "The World is your Oyster"
       href: Schedule.qmd
+    - section: "Community"
+      contents:       
+      - text: "AutoSpectral"
+        href: course/community/AutoSpectral/index.qmd  
+      - text: "TRU-OLS"
+        href: course/community/TRU-OLS/index.qmd
   page-footer: 
    left: Made with [Quarto](https://quarto.org/)
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diff --git a/course/01_InstallingRPackages/homeworks/jttoivon/cytomem.png b/course/01_InstallingRPackages/homeworks/jttoivon/cytomem.png