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Cosmetic fix for dropdown menu, couple word edits.
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@DavidRach
DavidRach committed Feb 7, 2025
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4 changes: 4 additions & 0 deletions Data.qmd
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Expand Up @@ -18,9 +18,13 @@ TheDate <- Sys.Date()
Dashboard data last updated on **`r TheDate`**

**Contents:**

**Gain and RCV** A .csv file containing the Daily Cytek QC data used for the Gain and RCV plots.

**MFI** A .csv file containing Gain and MFI information derrived from before and after Daily QC .fcs files.

**Gain and MFI** A .csv file containing Gain and MFI information derrived from Daily QC .fcs files.

**Plots** A .pdf file containing non-interactive version of all the plots for each instrument.

For additional information, navigate to the [Help](https://umgccfcss.github.io/InstrumentQC/help) page.
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14 changes: 7 additions & 7 deletions _quarto.yml
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Expand Up @@ -17,19 +17,19 @@ website:
href: index.qmd
- text: "Levey-Jennings Plots"
menu:
- text: "3L"
- text: "Cytek Aurora 3L"
href: Aurora3L.qmd
- text: "4L"
- text: "Cytek Aurora 4L"
href: Aurora4L.qmd
- text: "5L"
- text: "Cytek Aurora 5L"
href: Aurora5L.qmd
- text: "CS"
- text: "Cytek Aurora CS"
href: AuroraCS.qmd
- text: "Canto"
- text: "BD FACSCanto II "
href: CantoII.qmd
- text: "LSR"
- text: "BD LSR II"
href: LSRII.qmd
- text: "Aria"
- text: "BD FACSAria II"
href: AriaII.qmd
- text: "Data"
href: Data.qmd
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14 changes: 7 additions & 7 deletions docs/404.html
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<ul class="dropdown-menu" aria-labelledby="nav-menu-levey-jennings-plots">
<li>
<a class="dropdown-item" href="/InstrumentQC/Aurora3L.html">
<span class="dropdown-text">3L</span></a>
<span class="dropdown-text">Cytek Aurora 3L</span></a>
</li>
<li>
<a class="dropdown-item" href="/InstrumentQC/Aurora4L.html">
<span class="dropdown-text">4L</span></a>
<span class="dropdown-text">Cytek Aurora 4L</span></a>
</li>
<li>
<a class="dropdown-item" href="/InstrumentQC/Aurora5L.html">
<span class="dropdown-text">5L</span></a>
<span class="dropdown-text">Cytek Aurora 5L</span></a>
</li>
<li>
<a class="dropdown-item" href="/InstrumentQC/AuroraCS.html">
<span class="dropdown-text">CS</span></a>
<span class="dropdown-text">Cytek Aurora CS</span></a>
</li>
<li>
<a class="dropdown-item" href="/InstrumentQC/CantoII.html">
<span class="dropdown-text">Canto</span></a>
<span class="dropdown-text">BD FACSCanto II</span></a>
</li>
<li>
<a class="dropdown-item" href="/InstrumentQC/LSRII.html">
<span class="dropdown-text">LSR</span></a>
<span class="dropdown-text">BD LSR II</span></a>
</li>
<li>
<a class="dropdown-item" href="/InstrumentQC/AriaII.html">
<span class="dropdown-text">Aria</span></a>
<span class="dropdown-text">BD FACSAria II</span></a>
</li>
</ul>
</li>
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20 changes: 12 additions & 8 deletions docs/Data.html
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<ul class="dropdown-menu" aria-labelledby="nav-menu-levey-jennings-plots">
<li>
<a class="dropdown-item" href="./Aurora3L.html">
<span class="dropdown-text">3L</span></a>
<span class="dropdown-text">Cytek Aurora 3L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora4L.html">
<span class="dropdown-text">4L</span></a>
<span class="dropdown-text">Cytek Aurora 4L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora5L.html">
<span class="dropdown-text">5L</span></a>
<span class="dropdown-text">Cytek Aurora 5L</span></a>
</li>
<li>
<a class="dropdown-item" href="./AuroraCS.html">
<span class="dropdown-text">CS</span></a>
<span class="dropdown-text">Cytek Aurora CS</span></a>
</li>
<li>
<a class="dropdown-item" href="./CantoII.html">
<span class="dropdown-text">Canto</span></a>
<span class="dropdown-text">BD FACSCanto II</span></a>
</li>
<li>
<a class="dropdown-item" href="./LSRII.html">
<span class="dropdown-text">LSR</span></a>
<span class="dropdown-text">BD LSR II</span></a>
</li>
<li>
<a class="dropdown-item" href="./AriaII.html">
<span class="dropdown-text">Aria</span></a>
<span class="dropdown-text">BD FACSAria II</span></a>
</li>
</ul>
</li>
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</div>
</div></div><aside id="bslib-sidebar-1" class="sidebar html-fill-container html-fill-item"><div class="html-fill-container html-fill-item">
<p>Dashboard data last updated on <strong>2025-02-07</strong></p>
<p><strong>Contents:</strong> <strong>Gain and RCV</strong> A .csv file containing the Daily Cytek QC data used for the Gain and RCV plots. <strong>MFI</strong> A .csv file containing Gain and MFI information derrived from before and after Daily QC .fcs files. <strong>Gain and MFI</strong> A .csv file containing Gain and MFI information derrived from Daily QC .fcs files. <strong>Plots</strong> A .pdf file containing non-interactive version of all the plots for each instrument.</p>
<p><strong>Contents:</strong></p>
<p><strong>Gain and RCV</strong> A .csv file containing the Daily Cytek QC data used for the Gain and RCV plots.</p>
<p><strong>MFI</strong> A .csv file containing Gain and MFI information derrived from before and after Daily QC .fcs files.</p>
<p><strong>Gain and MFI</strong> A .csv file containing Gain and MFI information derrived from Daily QC .fcs files.</p>
<p><strong>Plots</strong> A .pdf file containing non-interactive version of all the plots for each instrument.</p>
<p>For additional information, navigate to the <a href="https://umgccfcss.github.io/InstrumentQC/help">Help</a> page.</p>
<p><strong>About</strong></p>
<p>This dashboard contains the visualized QC data for the Cytek Auroras at the <a href="https://www.medschool.umaryland.edu/cibr/core/umgccc_flow/">UMGCC FCSS</a></p>
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14 changes: 7 additions & 7 deletions docs/Examples_FlagRemoval.html
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<ul class="dropdown-menu" aria-labelledby="nav-menu-levey-jennings-plots">
<li>
<a class="dropdown-item" href="./Aurora3L.html">
<span class="dropdown-text">3L</span></a>
<span class="dropdown-text">Cytek Aurora 3L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora4L.html">
<span class="dropdown-text">4L</span></a>
<span class="dropdown-text">Cytek Aurora 4L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora5L.html">
<span class="dropdown-text">5L</span></a>
<span class="dropdown-text">Cytek Aurora 5L</span></a>
</li>
<li>
<a class="dropdown-item" href="./AuroraCS.html">
<span class="dropdown-text">CS</span></a>
<span class="dropdown-text">Cytek Aurora CS</span></a>
</li>
<li>
<a class="dropdown-item" href="./CantoII.html">
<span class="dropdown-text">Canto</span></a>
<span class="dropdown-text">BD FACSCanto II</span></a>
</li>
<li>
<a class="dropdown-item" href="./LSRII.html">
<span class="dropdown-text">LSR</span></a>
<span class="dropdown-text">BD LSR II</span></a>
</li>
<li>
<a class="dropdown-item" href="./AriaII.html">
<span class="dropdown-text">Aria</span></a>
<span class="dropdown-text">BD FACSAria II</span></a>
</li>
</ul>
</li>
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14 changes: 7 additions & 7 deletions docs/Examples_staff.html
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<ul class="dropdown-menu" aria-labelledby="nav-menu-levey-jennings-plots">
<li>
<a class="dropdown-item" href="./Aurora3L.html">
<span class="dropdown-text">3L</span></a>
<span class="dropdown-text">Cytek Aurora 3L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora4L.html">
<span class="dropdown-text">4L</span></a>
<span class="dropdown-text">Cytek Aurora 4L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora5L.html">
<span class="dropdown-text">5L</span></a>
<span class="dropdown-text">Cytek Aurora 5L</span></a>
</li>
<li>
<a class="dropdown-item" href="./AuroraCS.html">
<span class="dropdown-text">CS</span></a>
<span class="dropdown-text">Cytek Aurora CS</span></a>
</li>
<li>
<a class="dropdown-item" href="./CantoII.html">
<span class="dropdown-text">Canto</span></a>
<span class="dropdown-text">BD FACSCanto II</span></a>
</li>
<li>
<a class="dropdown-item" href="./LSRII.html">
<span class="dropdown-text">LSR</span></a>
<span class="dropdown-text">BD LSR II</span></a>
</li>
<li>
<a class="dropdown-item" href="./AriaII.html">
<span class="dropdown-text">Aria</span></a>
<span class="dropdown-text">BD FACSAria II</span></a>
</li>
</ul>
</li>
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34 changes: 17 additions & 17 deletions docs/Miscellaneous.html
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14 changes: 7 additions & 7 deletions docs/TaskSchedules.html
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<ul class="dropdown-menu" aria-labelledby="nav-menu-levey-jennings-plots">
<li>
<a class="dropdown-item" href="./Aurora3L.html">
<span class="dropdown-text">3L</span></a>
<span class="dropdown-text">Cytek Aurora 3L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora4L.html">
<span class="dropdown-text">4L</span></a>
<span class="dropdown-text">Cytek Aurora 4L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora5L.html">
<span class="dropdown-text">5L</span></a>
<span class="dropdown-text">Cytek Aurora 5L</span></a>
</li>
<li>
<a class="dropdown-item" href="./AuroraCS.html">
<span class="dropdown-text">CS</span></a>
<span class="dropdown-text">Cytek Aurora CS</span></a>
</li>
<li>
<a class="dropdown-item" href="./CantoII.html">
<span class="dropdown-text">Canto</span></a>
<span class="dropdown-text">BD FACSCanto II</span></a>
</li>
<li>
<a class="dropdown-item" href="./LSRII.html">
<span class="dropdown-text">LSR</span></a>
<span class="dropdown-text">BD LSR II</span></a>
</li>
<li>
<a class="dropdown-item" href="./AriaII.html">
<span class="dropdown-text">Aria</span></a>
<span class="dropdown-text">BD FACSAria II</span></a>
</li>
</ul>
</li>
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14 changes: 7 additions & 7 deletions docs/Usage.html
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<ul class="dropdown-menu" aria-labelledby="nav-menu-levey-jennings-plots">
<li>
<a class="dropdown-item" href="./Aurora3L.html">
<span class="dropdown-text">3L</span></a>
<span class="dropdown-text">Cytek Aurora 3L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora4L.html">
<span class="dropdown-text">4L</span></a>
<span class="dropdown-text">Cytek Aurora 4L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora5L.html">
<span class="dropdown-text">5L</span></a>
<span class="dropdown-text">Cytek Aurora 5L</span></a>
</li>
<li>
<a class="dropdown-item" href="./AuroraCS.html">
<span class="dropdown-text">CS</span></a>
<span class="dropdown-text">Cytek Aurora CS</span></a>
</li>
<li>
<a class="dropdown-item" href="./CantoII.html">
<span class="dropdown-text">Canto</span></a>
<span class="dropdown-text">BD FACSCanto II</span></a>
</li>
<li>
<a class="dropdown-item" href="./LSRII.html">
<span class="dropdown-text">LSR</span></a>
<span class="dropdown-text">BD LSR II</span></a>
</li>
<li>
<a class="dropdown-item" href="./AriaII.html">
<span class="dropdown-text">Aria</span></a>
<span class="dropdown-text">BD FACSAria II</span></a>
</li>
</ul>
</li>
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18 changes: 9 additions & 9 deletions docs/help.html
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<ul class="dropdown-menu" aria-labelledby="nav-menu-levey-jennings-plots">
<li>
<a class="dropdown-item" href="./Aurora3L.html">
<span class="dropdown-text">3L</span></a>
<span class="dropdown-text">Cytek Aurora 3L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora4L.html">
<span class="dropdown-text">4L</span></a>
<span class="dropdown-text">Cytek Aurora 4L</span></a>
</li>
<li>
<a class="dropdown-item" href="./Aurora5L.html">
<span class="dropdown-text">5L</span></a>
<span class="dropdown-text">Cytek Aurora 5L</span></a>
</li>
<li>
<a class="dropdown-item" href="./AuroraCS.html">
<span class="dropdown-text">CS</span></a>
<span class="dropdown-text">Cytek Aurora CS</span></a>
</li>
<li>
<a class="dropdown-item" href="./CantoII.html">
<span class="dropdown-text">Canto</span></a>
<span class="dropdown-text">BD FACSCanto II</span></a>
</li>
<li>
<a class="dropdown-item" href="./LSRII.html">
<span class="dropdown-text">LSR</span></a>
<span class="dropdown-text">BD LSR II</span></a>
</li>
<li>
<a class="dropdown-item" href="./AriaII.html">
<span class="dropdown-text">Aria</span></a>
<span class="dropdown-text">BD FACSAria II</span></a>
</li>
</ul>
</li>
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<p><img src="images/RCV_UV3.png" class="img-fluid quarto-figure quarto-figure-center figure-img"></p>
</figure>
</div>
<p>For Cytek instruments, a Daily QC fail is only triggered when %rCV exceeds either *% for SSC, or 6% for FSC and the following detectors: UV3, V3, B3, YG3, R3. When this happens, the instrument will appear as failed on the home page:</p>
<p>For Cytek instruments, a Daily QC fail is only triggered when %rCV exceeds either 8% for SSC, or 6% for FSC and the following detectors: UV3, V3, B3, YG3, R3. When this happens, the instrument will appear as failed on the home page:</p>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/InstrumentFail.png" class="img-fluid quarto-figure quarto-figure-center figure-img"></p>
Expand Down Expand Up @@ -306,7 +306,7 @@ <h1>Data</h1>
</div>
<p>Gain and %rCV links to .csv file containing those types of data.</p>
<p>MFI links to .csv file containing the data derrived from the before and after QC Bead .fcs files.</p>
<p>Both the above can be used if you want to (plot the data)[https://davidrach.github.io/Luciernaga/articles/QualityControl.html#qc_plots] yourself using a different ggplot2 color-scheme in R than the one we have selected. Additionally, data for timepoints older than the current year can be found here.</p>
<p>Both the above can be used if you want to <a href="https://davidrach.github.io/Luciernaga/articles/QualityControl.html#qc_plots">plot the data</a> yourself using a different ggplot2 color-scheme in R than the one we have selected. Additionally, data for timepoints older than the current year can be found here.</p>
<p>Plots is a .pdf containing static versions of all the interactive plots (MFI, Gain, %rCV) that are visible for the Levey-Jennings Plots for the individual instrument. QC fails appear as red squares, and vertical red dashed lines correspond to dates the field service engineer was on site for repairs or preventative maintenance.</p>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
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