UMGCCCFCSR · biancakbeck · Apr 7, 2026 · Apr 7, 2026 · Apr 7, 2026 · Apr 8, 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
@@ -96,7 +96,7 @@ Course materials can be found [here](/course/00_GitHub/index.qmd) or via the Cou
 
 ### Conference Break 1
 
-No class week of March 30, 2026. If you are attending the [ABRF conference](https://web.cvent.com/event/6aeb3907-0f0b-418d-a0d5-91f4de72c144/summary?RefId=ABRF%202026%20Annual%20Meeting%20Home%20Page), track me down at the [Complex Data Analysis in Flow Cytometry: Navigating the Landscape](https://web.cvent.com/event/6aeb3907-0f0b-418d-a0d5-91f4de72c144/websitePage:89d4bbd7-0f7c-4235-a335-97866af9506b) talk on Monday, March 30th at 4:30 PM. 
+No class week of March 30, 2026. If you are attending the [ABRF conference](https://web.cvent.com/event/6aeb3907-0f0b-418d-a0d5-91f4de72c144/summary?RefId=ABRF%202026%20Annual%20Meeting%20Home%20Page), track me down at the [Complex Data Analysis in Flow Cytometry: Navigating the Landscape](https://youtu.be/l9LQZ52gv3k?t=3678) talk on Monday, March 30th at 4:30 PM. 
 
 <br>
 <br>
@@ -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>
@@ -126,20 +126,29 @@ 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 27, 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>
 
-### Retrieving data for Statistics
+### Retrieving Data for Statistics
 
 ![](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: May 04, 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. 
 
 <br>
 <br>
 
+### Conference Break 2
+
+If you are attending the [Cyto conference](https://www.cytoconference.org/?gad_source=1&gad_campaignid=20633392465&gbraid=0AAAAADoJzsvHaLZAq9tqn_aTAQGEzIk_V&gclid=CjwKCAiA-sXMBhAOEiwAGGw6LJFFV69xaAU3s7bElL86RdnRNFwAYqOQO78MrIYQuG1qvRU6HTN3ZRoCGmAQAvD_BwE), track me down at my talks ([Open-Source automation](https://davidrach.github.io/abstracts.html#cyto-2026---flow-awarenesss) on June 7, 10:30-11:30AM at Grand Ballroom;
+and [Semi-supervised pipeline](https://davidrach.github.io/abstracts.html#cyto-2026---alpha-beta) on June 9, 10:30-11:45AM atRoom 2DEF) or poster (grab some Cytometry in R course hex stickers!) 
+
+<br>
+<br>
+
+
 ### Spectral Signatures
 
 ![](images/Signatures.png){width=75%}
@@ -185,13 +194,6 @@ No class week of March 30, 2026. If you are attending the [ABRF conference](http
 <br>
 <br>
 
-### Conference Break 2
-
-No class week of June 8, 2026. If you are attending the [Cyto conference](https://www.cytoconference.org/?gad_source=1&gad_campaignid=20633392465&gbraid=0AAAAADoJzsvHaLZAq9tqn_aTAQGEzIk_V&gclid=CjwKCAiA-sXMBhAOEiwAGGw6LJFFV69xaAU3s7bElL86RdnRNFwAYqOQO78MrIYQuG1qvRU6HTN3ZRoCGmAQAvD_BwE), track me down at my talks ([Open-Source automation](https://davidrach.github.io/abstracts.html#cyto-2026---flow-awarenesss) on June 7, 10:30-11:30AM at Grand Ballroom;
-and [Semi-supervised pipeline](https://davidrach.github.io/abstracts.html#cyto-2026---alpha-beta) on June 9, 10:30-11:45AM atRoom 2DEF) or poster (grab some Cytometry in R course hex stickers!) 
-
-<br>
-<br>
 
 ### Normalization: Batch Effect or Real Biology
 
@@ -220,6 +222,14 @@ and [Semi-supervised pipeline](https://davidrach.github.io/abstracts.html#cyto-2
 <br>
 <br>
 
+### Conference Break 3
+
+No class week of August 10, 2026. If you are attending the [BioC conference](https://bioc2026.bioconductor.org/), track me down at my [short talk](https://bioc2026.bioconductor.org/schedule/) on Monday, August 10th from 11:00-12:15pm. 
+
+<br>
+<br>
+
+
 ### The Art of GitHub Diving
 
 ![](https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcTE3IHi5Y2itTmH60RF81y5b8JnSeeJvTTATA&s){width=100%}
@@ -265,13 +275,6 @@ and [Semi-supervised pipeline](https://davidrach.github.io/abstracts.html#cyto-2
 <br>
 <br>
 
-### Conference Break 3
-
-No class week of August 10, 2026. If you are attending the [BioC conference](https://bioc2026.bioconductor.org/), track me down at my talk/poster. 
-
-<br>
-<br>
-
 ### Reproducibility and Replicability
 
 ![](https://media.springernature.com/lw1200/springer-static/image/art%3A10.1038%2F533452a/MediaObjects/41586_2016_BF533452a_Fige_HTML.jpg){width=50%}

diff --git a/_quarto.yml b/_quarto.yml
@@ -6,15 +6,23 @@ project:
     - Schedule.qmd
     - ExistingResources.qmd
     - PackageWalkthroughs.qmd
+    - Homeworks.qmd
+    - Announcements.qmd
     - course/index.qmd
+    - course/TakeAwayGallery.qmd
     - 00_*
     - 01_*
     - 02_*
     - 03_*
     - 04_*
     - 05_*
     - 06_*
-    - 07_*    
+    - 07_*   
+    - 08_* 
+    - 09_*
+    - 10_*
+    - 11_*
+    - course/community/**/*.qmd
 website:
   google-analytics: "G-LZ35J3XE4D"
   announcement: 
@@ -35,11 +43,15 @@ website:
         href: Schedule.qmd
       - text: "Course"
         href: course/index.qmd
+      - text: "Announcements"
+        href: Announcements.qmd        
     right:
     - text: Existing Resources
       href: ExistingResources.qmd
     - text: Discussions
       href: https://github.com/UMGCCCFCSR/CytometryInR/discussions
+    - text: Homeworks
+      href: Homeworks.qmd
     - icon: youtube
       href: https://www.youtube.com/@CytometryInR
       aria-label: YouTube
@@ -82,12 +94,30 @@ 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: "Bonus Content"
+      contents: 
+      - text: "Concatenate - Extended Cut"
+        href: course/10_Downsampling/concatenate.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/)
    right: |

diff --git a/course/01_InstallingRPackages/homeworks/biancakbeck/homeworkWEEK1.qmd b/course/01_InstallingRPackages/homeworks/biancakbeck/homeworkWEEK1.qmd
@@ -0,0 +1,41 @@
+Problem 1
+We installed PeacoQC during this session, but we didn’t have time to explore what functions are present within the package. Using what you have learned about accessing documentation, figure out and list what functions it contains
+```{r}
+library(PeacoQC)
+?PeacoQC
+```
+
+Problem 2
+Take a closer look at the list of Bioconductor cytometry packages. Report back on how many there are currently in Bioconductor, the author/maintainer with the most contributed cytometry R packages, and a couple packages that you would be interested in exploring more in-depth later in the course.
+
+```{r}
+#I saved a screenshot in the folder showing how many cytometry related packages I found.
+
+#One of the most active contributors appears to be the RGLab developer group, which maintains several core cytometry packages such as flowCore, flowWorkspace, openCyto, CytoML, and ggcyto. I would be interested in exploring further CytoML for FlowJo integration
+
+```
+
+Problem 3
+There is another way to install R packages, using the newer pak package. Positron uses this when installing suggested dependencies.
+
+After learning more about it via the documentation and it’s pkgdown website, I would like you to attempt to install the following three R packages using this newer method: “broom”, “cytoMEM”, “DillonHammill/CytoExploreR”.
+
+Take screenshots, and in a new quarto markdown document, describe how the installation process differed from what you saw for install.packages(), install() and install_github().
+
+
+```{r}
+install.packages("pak")
+library(remote)
+library(pak)
+
+pak::pkg_install("broom")
+pak::pkg_install("cytoMEM")
+pak::pkg_install("DillonHammill/CytoExploreR")
+
+#I actually didn´t find it so different, to me, it looks like it took more time to install but it also showed how was going the installation step by step
+
+#I could not install CytoExploreR by pak but it was possible with the install_github
+
+remotes::install_github("DillonHammill/CytoExploreR")
+
+```
diff --git a/course/01_InstallingRPackages/homeworks/biancakbeck/image.png b/course/01_InstallingRPackages/homeworks/biancakbeck/image.png
diff --git a/course/01_InstallingRPackages/index.qmd b/course/01_InstallingRPackages/index.qmd
@@ -30,6 +30,8 @@ Before getting started, please make sure you have completed the creating a [GitH
 
 :::{.callout-important}
 Please make sure to [sync](/course/00_Homeworks/index.qmd#sync-your-fork) your forked version of the CytometryInR repository, and [pull](/course/00_Git/index.qmd#pull) any changes to your local computer's CytometryInR project folder so that you have the most recent version of the code and data available. 
+
+For YouTube walkthrough of this process, click [here](https://www.youtube.com/live/Zfctacqpe90?si=a7Ad61kj6_UDNkGw&t=32)
 :::
 
 <br>

diff --git a/course/01_InstallingRPackages/slides.qmd b/course/01_InstallingRPackages/slides.qmd
@@ -37,6 +37,7 @@ Before getting started, please make sure you have completed the creating a [GitH
 
 Please make sure to [sync](/course/00_Homeworks/index.qmd#sync-your-fork) your forked version of the CytometryInR repository, and [pull](/course/00_Git/index.qmd#pull) any changes to your local computer's CytometryInR project folder so that you have the most recent version of the code and data available. 
 
+For YouTube walkthrough of this process, click [here](https://www.youtube.com/live/Zfctacqpe90?si=a7Ad61kj6_UDNkGw&t=32)
 :::
 :::
 

diff --git a/course/02_FilePaths/homeworks/biancakbeck/homeworkWEEK2.qmd b/course/02_FilePaths/homeworks/biancakbeck/homeworkWEEK2.qmd
@@ -0,0 +1,70 @@
+Problem 1
+Plug in an external hard-drive or USB into your computer. Manually, create a folder within called “TargetFolder”. Try to programmatically specify the file path to identify the folders and files present on your external drive. Then, try to copy your .fcs files from their current folder on your desktop to the TargetFolder on your drive using R. Remember, just copy, no deletion, you need to walk before you can run :D
+
+```{r}
+getwd()
+FolderLocation <- "D:/TargetFolder"
+FolderLocation
+list.files(FolderLocation)
+files_fcs <- list.files("D:/TargetFolder", pattern=".fcs", full.names=TRUE,recursive=FALSE)
+files_fcs
+
+Desktop <- "c:/Users/biihb/desktop"
+list.files(Desktop)
+file.copy(from=files_fcs , to=Desktop)
+
+```
+
+Problem 2
+In this session, we used list.files() with the “full.names argument” set to TRUE, as well as the basename() function to identify specific files. But what if you wanted a particular directory. Run list.files() with “full.names argument” and “recursive” argument set to TRUE, and then search online to find an R function that would retrieve the “” individual directory folders.
+
+```{r}
+all_items <- list.files(
+  path = "D:/TargetFolder",
+  full.names = TRUE,
+  recursive = TRUE
+)
+
+all_items
+
+list.dirs()
+all_dirs <- list.dirs(
+  path = "D:/TargetFolder",
+  full.names = TRUE,
+  recursive = TRUE
+)
+
+all_dirs
+#After using list.files() with full.names = TRUE and recursive = TRUE, I searched for a function that specifically retrieves directories instead of files. I found that the list.dirs() function in base R can be used to return only folder paths. This function supports recursive searching and full path retrieval similarly to list.files()
+```
+
+Problem 3
+R packages often come with internal datasets, that are typically used for use in the help documentation examples. These can be accessed through the use of the system.file() function. See an example below.
+
+system.file("extdata", package = "FlowSOM")
+
+Using what we have learned about file.path navigation, search your way down the file.directory of the FlowSOM and flowWorkspace packages, and identify any .fcs files that are present for use in the documentation.
+
+```{r}
+library(flowWorkspace)
+library(FlowSOM)
+system.file("extdata", package = "FlowSOM")
+FlowSOM_path <- system.file("extdata", package = "FlowSOM")
+
+FlowSOM_path
+list.files(
+  FlowSOM_path,
+  pattern = "\\.fcs$",
+  full.names = TRUE,
+  recursive = TRUE
+)
+#I found 1 archive : [1] "C:/Users/biihb/AppData/Local/R/win-library/4.5/FlowSOM/extdata/68983.fcs"
+
+system.file("extdata", package = "flowWorkspace")
+flowWorkspace_path <- system.file("extdata", package = "flowWorkspace")
+flowWorkspace_path
+
+list.files(flowWorkspace_path, pattern = ".fcs", full.names = TRUE, recursive = TRUE)
+
+#I did not find any
+```
-Original file line number
+Diff line change
@@ Expand Up @@
     :::{.callout-important}
     Please make sure to [sync](/course/00_Homeworks/index.qmd#sync-your-fork) your forked version of the CytometryInR repository, and [pull](/course/00_Git/index.qmd#pull) any changes to your local computer's CytometryInR project folder so that you have the most recent version of the code and data available.
+    For YouTube walkthrough of this process, click [here](https://www.youtube.com/live/Zfctacqpe90?si=a7Ad61kj6_UDNkGw&t=32)
     :::
     <br>
@@ Expand Down @@