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

Half the world writes 0.5 and half writes 0,5, and a qPCR platform has to work for both without ever changing the number. Clarida resolves this asymmetrically: it accepts either separator when you type, and always shows and exports a point. This note explains the rule, why entry and display are governed differently, and the one case Clarida deliberately refuses to interpret — digit grouping, where 1,234 could mean two very different quantities.

Before a plate is laid out or data is imported, an experiment needs to know which samples and which assays it contains. Both can be typed in, generated as a series, taken from your library, or pasted from a spreadsheet. Pasting is the fastest route for a real experiment, and it does more than carry names: a header row lets you set types, quantities and their units, positions and quality-control limits in the same paste, and any column Clarida does not recognise becomes a custom property on every row. That is how a property is set on many samples at once.

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.

Getting a qPCR run into analysis software usually means exporting on the instrument PC, then copying that file to a memory stick or emailing it to yourself. Porta is a small program that runs on the instrument PC and makes the folders you choose visible inside Clarida, so you can import a run straight from where the instrument wrote it. On a Roche LightCycler 480 it can go further and read finished runs from the instrument itself, with no export step. This page covers what it does, how you use it week to week, and how to set it up.

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.