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quicR

Description

quicR is a package made for the analysis of real-time quaking-induced conversion (RT-QuIC) assays.

Much of the functionality is designed to be integrated with the Excel output files generated by the BMG analysis software, MARS. For best results, in the MARS software select:

flowchart TB
excel(Excel Export)

subgraph A[Select the following export options]
  direction LR
  micro(Microplate View)
  table(Table View)
  trans(Transpose Table)
  test(Add test run \n information)
end

export(Export report to Excel)

excel --> A
micro --> table --> trans --> test
A --> export

Having both the microplate view and the table view helps with integrating plate layouts and the real-time data.

For many of the functions, it is important to have a table labelled “Sample IDs” on the microplate view sheet of the Excel file.

Examples

Plate IDs for BMG Import

Use BMG_format.R script to format a .CSV file with a Sample IDs in a plate view into a format importable into the BMG control software.

For example .CSV file, see:

tests -> testthat -> BMG_formatting -> plate_layout.csv

The file, “formatted.txt” in the same folder, is how the export should look to be imported into the BMG software.

Plate View

Use plate_view_export.R to export a plate view of the real-time data from an Excel file made in MARS.

For example .CSV files, see:

tests -> testthat -> input_files

Calculations

The program, calculate_metrics.R, will calculate relevant metrics such as maxpoint ratio, max slope, time-to-threshold, and rate of amyloid formation.

An Excel file will also be created with the full data and summarized data. A plot of the summarized data will also be created.

For example .CSV files, see:

tests -> testthat -> input_files

Author

Gage Rowden

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.