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Homework week 11 lk #212

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39 changes: 21 additions & 18 deletions Schedule.qmd
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Expand Up @@ -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>
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Expand Down Expand Up @@ -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 [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.
[**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 [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.
[**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%}
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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%}
Expand Down Expand Up @@ -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%}
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4 changes: 4 additions & 0 deletions _quarto.yml
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Expand Up @@ -108,6 +108,10 @@ website:
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"
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