Know how your data is being handled. Every decision, documented.

Bringing instrument data into an experiment in Clarida means importing the Cq export your instrument software already produced. If that import is well annotated, that is all it takes to start downstream analyses. If the experiment was designed in Clarida, two extra steps link the Cq data to the pre-generated annotation and resolve any annotation conflicts. We describe what kind of data Clarida imports today and how the importer adapts to the workflow: a single step when going straight to analysis, two more when there is a design to reconcile against.

Exploration is the open-ended part of qPCR analysis: looking at your relative quantities from several angles to see what the data is telling you. We describe how Clarida keeps this exploratory mode deliberately separate from formal statistical testing, why that separation protects against p-hacking, and how any view worth keeping can be frozen into an annotated, citable snapshot for reporting.

Plate layout annotation is a repetitive, error-prone step in qPCR experiment preparation that most researchers handle manually. We show that four well-chosen parameters — block grouping, orientation, style, and replicate placement — are sufficient to automatically generate well annotations for the majority of practical use cases while respecting individual lab preferences and pipetting workflows.