add qpcr workflow documentation

EPPIcenter · Oct 31, 2024 · 38c8348 · 38c8348
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diff --git a/vignettes/Searching-SampleDB.Rmd b/vignettes/Searching-SampleDB.Rmd
@@ -195,7 +195,7 @@ plate and will return the information detailed below.
 Cryovials can be searched for using the same filters as micronix
 samples.
 
-### Search Controls (DBS & WB)
+### Search for Controls and Extractions (DBS & WB)
 
 Uploaded Dry Blood Spots and Whole Blood tubes can be viewed in the
 "Search, Archive & Delete" Panel after selecting "Controls" under
@@ -216,7 +216,7 @@ samples.
 Extracted controls are tied to controls in the database by the `Control UID`
 and the `Batch`. With these two identifiers, you can find the exact control
 that an extraction was derived from (and vice versa). The following will go
-over how to do both workflows
+over how to do both workflows.
 
 ##### Find the control used in an extraction
 

diff --git a/vignettes/qPCR Workflow.Rmd b/vignettes/qPCR Workflow.Rmd
@@ -0,0 +1,74 @@
+---
+title: 'SampleDB qPCR Workflow'
+output: rmarkdown::html_document
+vignette: >
+  %\VignetteIndexEntry{qPCR Workflow}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+The section below will cover how to download a qPCR template for the QuantStudio3 Thermocycler. 
+
+## Preparing your plate in SampleDB
+
+```
+Please review `How to Move Samples and Controls` page for more information on how to move samples and controls.
+```
+
+In order for SampleDB to generate a qPCR template for a plate, the plate <em>in SampleDB</em> must meet the following criteria.
+
+1. Only controls may exist in wells A11-E11, and must be arranged in descending order by concentration.
+2. Wells A12-E12 are to remain empty.
+3. Wells H11 and H12 are reserved for the negative control.
+
+These requirements are in place to ensure that samples and controls keep their metadata linked throughout the qPCR process by enforcing a standard layout. We use <em>Biological Replicates</em> for our controls and let SampleDB record the replicates in wells A12-E12 using information about the controls in wells A11-E11. These are the only requirements and will be checked (see 'Validation Details' below). You may have samples, controls or empty wells in wells A1-H10, F11-F12 and G11-G12.
+
+You should scan your plate with the Traxcer scanner and generate a 'Move' file. Once completed, you should see your plate in the search panel with your samples and extracted controls.
+
+## Downloading a qPCR Template
+
+To begin the download, start by searching for your plate. If you attempt to start the process without searching for a plate, SampleDB will stop you.
+
+![](qPCR_StartButton.png)
+
+You are allowed to have missing samples. If you do not have a sample in wells A1-H10, you will see the dialog below. Press 'Okay' to continue if you should have missing samples in the reported wells.
+
+![](qPCR_MissingSamples.png)
+
+Controls are expected to decrement. In wells A11-E11, you are expected to have controls with densities <em>near</em> 10K, 1K, 100, 10, and 1 p / uL, respectively. The densities do not have to be exact. You will see the dialog below if SampleDB detects that the specified control does not have the expected density given it's position.
+
+If everything looks okay, press 'Okay' to continue.
+
+![](qPCR_DensityMismatch.png)
+
+Finally, you will see a color-coded visualization of your plate. Wells with samples will be yellow and will have the micronix barcode and specimen type recorded in the cell. Wells with controls will be green and will have the micronix barcode, specimen type <em>and</em> density recorded. Wells that are empty with have no text and will be grey. 
+
+The negative control (wells H11-H12) will say NTC in the first two rows (where other wells have a micronix barcode and specimen type), and will say 'Negative' in the third row where the density is ususally recorded.
+
+<em>Proper image to be added here...</em>
+
+If everything looks correct, press 'Download qPCR Table'. A tab-deliminited text file will be generated for you.
+
+## How to upload your template to QuantStudio3 ThermoCycler
+
+**You will need make sure the file is located on the computer that is controlling the thermocycler.**
+
+Once you've opened the application, go to 'File' > 'Import Plate Experiment'. Enter the file that you have downloaded.
+
+You should see a success dialog box, and your uploaded plate.
+
+![](qPCR_QuantStudio_PostUpload.png)
+
+## Validation Details
+
+There are two validation errors you may see.
+
+### "Non-control in a standard position."
+
+This means that there is a sample in wells A11-E11, which are reserved for controls, or in wells H11-H12, which are reserved for the negative controls.
+
+### "Empty well in a standard position (non-NTC)."
+
+This means that a control is missing in wells A11-E11.
+
diff --git a/vignettes/qPCR_BP_2024-10-30.txt b/vignettes/qPCR_BP_2024-10-30.txt
@@ -0,0 +1,98 @@
+[Sample Setup]										
+Well	Well Position	Sample Name	Biogroup Name	Biogroup Color	Target Name	Task	Reporter	Quencher	Quantity	Comments
+1	A1	8068287454	DDIC-014-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+2	A2	8068287452	DDIC-009-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+3	A3	8068287093	DDUIC-033-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+4	A4	8068286936	DDUIC-017-C3-F04		VarATS	UNKNOWN	FAM	NFQ-MGB		
+5	A5	8068287445	DDUIC-030-C2-F03		VarATS	UNKNOWN	FAM	NFQ-MGB		
+6	A6	8068286984	DDUIC-032-C3-F03		VarATS	UNKNOWN	FAM	NFQ-MGB		
+7	A7	8068287150	DDIC-025-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+8	A8	8068287092	DDUIC-034-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+9	A9	8068287455	DDIC-035-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+10	A10	8068286981	DDIC-026-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+11	A11	7395820416	10000		VarATS	STANDARD	FAM	NFQ-MGB	"1e+04"	BP TEST
+12	A12	7395820416	10000		VarATS	STANDARD	FAM	NFQ-MGB	"1e+04"	BP TEST
+13	B1	8068287311	DDIC-016-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+14	B2	8068286870	DDIC-038-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+15	B3	8068286920	DDIC-001-C2-F03		VarATS	UNKNOWN	FAM	NFQ-MGB		
+16	B4	8068287457	DDUIC-030-C3-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+17	B5	8068287255	DDUIC-028-C3-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+18	B6	8068286960	DDIC-011-F02		VarATS	UNKNOWN	FAM	NFQ-MGB		
+19	B7	8068287166	DDUIC-024-C3-F04		VarATS	UNKNOWN	FAM	NFQ-MGB		
+20	B8	8068286933	DDUIC-032-C2-F04		VarATS	UNKNOWN	FAM	NFQ-MGB		
+21	B9	8068287343	DDIC-022-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+22	B10	8068287264	DDUIC-017-C3-F05		VarATS	UNKNOWN	FAM	NFQ-MGB		
+23	B11	8203749561	1000		VarATS	STANDARD	FAM	NFQ-MGB	"1e+03"	BP TEST
+24	B12	8203749561	1000		VarATS	STANDARD	FAM	NFQ-MGB	"1e+03"	BP TEST
+25	C1	8068287102	DDIC-027-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+26	C2	8068286996	DDIC-044-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+27	C3	8068286788	DDUIC-036-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+28	C4	8068287273	DDIC-031-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+29	C5	8068286961	DDIC-013-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+30	C6	8068287182	DDUIC-016-C2-F02		VarATS	UNKNOWN	FAM	NFQ-MGB		
+31	C7	8068286812	DDUIC-015-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+32	C8	8068287157	DDIC-021-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+33	C9	8068287481	DDUIC-028-C3-F03		VarATS	UNKNOWN	FAM	NFQ-MGB		
+34	C10	8068286982	DDUIC-019-C1-F05		VarATS	UNKNOWN	FAM	NFQ-MGB		
+35	C11	4739056827	100		VarATS	STANDARD	FAM	NFQ-MGB	"1e+02"	BP TEST
+36	C12	4739056827	100		VarATS	STANDARD	FAM	NFQ-MGB	"1e+02"	BP TEST
+37	D1	8068287063	DDIC-038-F02		VarATS	UNKNOWN	FAM	NFQ-MGB		
+38	D2	8068287001	DDUIC-026-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+39	D3	8068287245	DDUIC-019-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+40	D4	8068287008	DDIC-045-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+41	D5	8068286983	DDIC-036-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+42	D6	8068287380	DDIC-015-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+43	D7	8068287387	DDIC-043-F02		VarATS	UNKNOWN	FAM	NFQ-MGB		
+44	D8	8068286932	DDUIC-008-C3-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+45	D9	8068286683	DDIC-028-F02		VarATS	UNKNOWN	FAM	NFQ-MGB		
+46	D10	8068287110	DDUIC-017-C2-F03		VarATS	UNKNOWN	FAM	NFQ-MGB		
+47	D11	5102734896	10		VarATS	STANDARD	FAM	NFQ-MGB	"1e+01"	BP TEST
+48	D12	5102734896	10		VarATS	STANDARD	FAM	NFQ-MGB	"1e+01"	BP TEST
+49	E1	8068286944	DDUIC-009-F03		VarATS	UNKNOWN	FAM	NFQ-MGB		
+50	E2	8068287006	DDIC-020-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+51	E3	8068287262	DDUIC-032-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+52	E4	8068287061	DDUIC-030-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+53	E5	8068286899	DDIC-041-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+54	E6	8068287147	DDUIC-017-C3-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+55	E7	8068287346	DDIC-003-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+56	E8	8068286700	DDUIC-010-C1-F02		VarATS	UNKNOWN	FAM	NFQ-MGB		
+57	E9	8068286779	DDIC-040-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+58	E10	8068287397	DDIC-006-F04		VarATS	UNKNOWN	FAM	NFQ-MGB		
+59	E11	9482035716	1		VarATS	STANDARD	FAM	NFQ-MGB	"1e+00"	BP TEST
+60	E12	9482035716	1		VarATS	STANDARD	FAM	NFQ-MGB	"1e+00"	BP TEST
+61	F1	8068286773	DDUIC-017-C3-F06		VarATS	UNKNOWN	FAM	NFQ-MGB		
+62	F2	8068286889	DDIC-005-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+63	F3	8068286970	DDUIC-032-C3-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+64	F4	8068287077	DDUIC-011-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+65	F5	8068287248	DDIC-008-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+66	F6	8068287362	DDIC-009-F02		VarATS	UNKNOWN	FAM	NFQ-MGB		
+67	F7	8068286874	DDIC-011-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+68	F8	8068286985	DDUIC-029-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+69	F9	8068287192	DDIC-030-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+70	F10	8068286680	DDUIC-006-C1-F01		VarATS	UNKNOWN	FAM	NFQ-MGB		
+71	F11	1052938476	0.1		VarATS	STANDARD	FAM	NFQ-MGB	"1e-01"	BP TEST
+72	F12	1052938476	0.1		VarATS	STANDARD	FAM	NFQ-MGB	"1e-01"	BP TEST
+73	G1									
+74	G2									
+75	G3									
+76	G4									
+77	G5									
+78	G6									
+79	G7									
+80	G8									
+81	G9									
+82	G10									
+83	G11									
+84	G12									
+85	H1									
+86	H2									
+87	H3									
+88	H4									
+89	H5									
+90	H6									
+91	H7									
+92	H8									
+93	H9									
+94	H10									
+95	H11	NTC	NTC		VarATS	NTC	FAM	NFQ-MGB		
+96	H12	NTC	NTC		VarATS	NTC	FAM	NFQ-MGB		
diff --git a/vignettes/qPCR_DensityMismatch.png b/vignettes/qPCR_DensityMismatch.png
diff --git a/vignettes/qPCR_MissingSamples.png b/vignettes/qPCR_MissingSamples.png
diff --git a/vignettes/qPCR_PlateViz.png b/vignettes/qPCR_PlateViz.png
diff --git a/vignettes/qPCR_QuantStudio_PostUpload.png b/vignettes/qPCR_QuantStudio_PostUpload.png
diff --git a/vignettes/qPCR_StartButton.png b/vignettes/qPCR_StartButton.png