A QuantStudio Design and Analysis alternative for the analysis half
Design and Analysis does two jobs: it sets up the plate and it analyses the result. The first job belongs on the instrument. The second can happen anywhere, if your tool can read the run file.
If you want to keep QuantStudio for running plates but analyse elsewhere, you need a tool that reads the original .eds file, not just a CSV export. CycleView does that on Mac and Windows: it opens the run with plate layout and raw fluorescence, lets you set threshold and baseline, runs ΔΔCt with reference genes and statistics, and exports SVG figures and RDML. Free CSV-based tools such as LinRegPCR are strong for efficiency analysis but start from an export and lose the plate context.
What you actually need from an alternative
Most people looking for an alternative do not want to replace the instrument software. They want to stop booking the instrument PC to do analysis. That means the alternative must:
- open the original run file, so curves can be checked and Cq recalculated;
- run where you work, often on a Mac;
- do the relative quantification you need, which for most groups is ΔΔCt;
- produce figures you can put in a paper without rebuilding them in another program.
How the options compare
| Tool | Input | Mac | ΔΔCt | Figures | Price |
|---|---|---|---|---|---|
| Vendor desktop software | Own run files | No | Yes | Basic | Bundled |
| Qraphics | CSV export | Yes | Yes | Yes | $29.99 |
| LinRegPCR / ProntoPCR | CSV export | Partly | Partly | No | Free |
| CycleView | .eds, .ixo, .lc96p, .rex, RDML | Yes | Yes, with stats | SVG / PNG | Free viewer, Pro $12/mo |
Why the original file matters
A CSV of Cq values is a summary. Once you are holding only the summary, you can no longer see that one replicate amplified late because of a bubble, that the baseline window caught the start of the exponential phase, or that the NTC shows a primer-dimer melt peak. Those are exactly the things a reviewer asks about, and the MIQE guidelines expect you to be able to report them.
Keep both, use each for its job
The practical setup in most labs: the instrument PC runs plates and saves .eds files to a shared drive. Everyone analyses from there on their own computer. Nobody queues for the instrument PC to move a threshold, and the run file remains the single source of truth.
Open your run on your own laptop
CycleView opens QuantStudio, LightCycler, Rotor-Gene and RDML files on Mac and Windows. The viewer is free, and nothing is uploaded.
Get CycleView
Mac and Windows · runs locally · for research use, not for diagnosis.
FAQ
Will CycleView give the same Cq values as the vendor software?
With the same threshold and baseline, Cq values should agree closely. Different automatic baseline algorithms can shift Cq slightly, so set threshold and baseline explicitly when you compare.
Can it do standard-curve absolute quantification?
CycleView focuses on curve review, Cq and ΔΔCt relative quantification, figures and export.
Can several people in the lab use it?
Yes. The Lab plan covers five seats for $49 a month, with shared analysis templates per assay.