Click-Prep: An Interactive Data Preparation Tool for Click-qPCR

Abstract Click-qPCR is a browser-based application for relative qPCR analysis that requires a tidy-format CSV file containing four columns: sample, group, gene, and Cq. Preparing this input from qPCR instrument output typically requires manual reformatting and calculation of mean Cq values for technical replicates. To simplify this process, we developed Click-Prep ( https://kubo-azu.shinyapps.io/Click-Prep/ ), an interactive web-based application designed specifically to create Click-qPCR input files. Click-Prep imports CSV, TXT, TSV, and XLS/XLSX files and supports skipping of instrument-generated metadata rows, interactive column mapping, and manual assignment of experimental groups. Users can review technical-replicate measurements, exclude selected rows according to predefined quality-control criteria, and calculate mean Cq values for each sample– group–target combination. Missing or nonnumeric Cq values are flagged for review and must be resolved before the mean is calculated. Click-Prep can also combine compatible formatted CSV files, such as datasets obtained from separate qPCR plates. The resulting dataset is exported as a standardized CSV file containing the four fields required by Click-qPCR. By integrating these operations into a guided browser-based workflow, Click-Prep enables users to prepare Click-qPCR input files rapidly and consistently without programming. Key features Creates standardized Click-qPCR input files containing sample, group, gene, and Cq columns. Imports tabular qPCR instrument output and supports metadata-row skipping, interactive column mapping, and manual group assignment. Supports user-controlled review and exclusion of technical-replicate measurements and calculation of mean Cq values. Combines compatible mean Cq datasets from multiple qPCR plates into a single Click-qPCR input file. Graphical overview