What happened to qbase+. Written by the person who built it, and what he built instead.

For more than 15 years, qbase+ was the qPCR analysis software researchers reached for when they needed reliable, MIQE-compliant qPCR data analysis. It wasn't perfect, but it did the job well: efficiency-corrected normalization, reference gene stability analysis via geNorm, inter-run calibration, and results you could trust and report.

qbase+ itself has been cited in roughly 3,000 papers. The underlying methods it implemented, on reference gene normalization, efficiency correction, and qPCR best practice, span tens of thousands of citations across the broader field. Labs worldwide built their qPCR analysis workflows around it. I know, because I built it, and I spent years watching researchers use it in ways I hadn't anticipated, for experiments I hadn't imagined, in labs I'd never visited.

I'm Jan Hellemans. I co-founded Biogazelle with Jo Vandesompele. We built qbase+ together. And I want to be straightforward with you about what happened to it.

In 2021, Biogazelle was acquired by CellCarta, a contract research organization focused on genomics services. The acquisition made sense commercially. But qbase+, a software product, was never CellCarta's core business.

For a period after the acquisition, a free version of qbase+ remained available on the CellCarta website. It kept existing users running. But it wasn't being actively developed, maintained, or supported. No new features. No bug fixes. No roadmap. Eventually, that version was deprecated too. qbase+, also known as qbasePLUS, reflecting its original URL at qbaseplus.com, is no longer available for download anywhere.

That left a gap. Researchers who had built their normalization workflows around qbase+, who relied on geNorm for reference gene selection, who used inter-run calibration across multi-plate experiments, who trusted its MIQE compliance, suddenly had no clear path forward.

The ResearchGate threads tell the story plainly. “qbase+ is not available anymore since the company was bought by CellCarta. What is the alternative?” That question sat unanswered. No one with real knowledge of the tool was responding. The team that understood it was no longer involved.

That bothered me.

qbase+ wasn't just a piece of software. It was an implementation of scientific methodology that took years to develop and validate. The geNorm algorithm developed by Jo Vandesompele, published in Genome Biology in 2002, now cited more than 20,000 times, is the foundation of how most labs select reference genes for normalization. The qBase quantification framework I published in 2007 formalized the mathematical framework for efficiency correction and inter-run calibration, and helped establish them as standard practice in qPCR analysis. These are among the foundational contributions to the field. There is a much broader body of work behind them, from many researchers, built up over decades.

These aren't features. They're the scientific foundations of reliable qPCR analysis. When the software that implemented them disappeared, the question wasn't just “what tool do I use?” It was “how do I keep doing this correctly?”

That's a question I feel a responsibility to answer. Not because I own those methods. They belong to the scientific community. But because I understand them, and because walking away from that responsibility didn't feel right.

Clarida is what we built when we had the chance to start over, with everything we learned from qbase+, and everything we wished it had been. The thinking behind it is laid out in our manifesto.

The scientific foundations are the same: geNorm for reference gene selection, efficiency-corrected normalization, inter-run calibration, MIQE compliance. The Analyze stage is being built to that standard, and beyond it. Everything qbase+ was, and more. The result is qPCR normalization software built on the same validated methods, by the same people.

But Clarida goes further than qbase+ ever did. qbase+ was an analysis tool. You brought your data to it after the experiment. Clarida starts before the experiment: from defining your biological question, through designing your plate, to guiding your wet lab protocol, through analysis, through to a publication-ready report with a MIQE-compliant methods section drafted from your actual experiment record.

That's the D-DEAR framework: Define, Design, Execute, Analyze, Report. Five connected stages. No gaps. No re-entry. No lost context between steps.

Not replacing how you work. Connecting what's been disconnected.

geNorm is available as a free tool in Clarida right now. The algorithm is the same, the one from Jo's 2002 paper, the one that's been validated in tens of thousands of experiments. The interface is modern. The results will feed directly into your normalization without any export or reformatting step.

If geNorm was the main reason you used qbase+, or if you're looking for a geNorm alternative more broadly, that's where to start.

Clarida is in early access. The Analyze stage, the part most comparable to qbase+, is functional and solid. The full D-DEAR pipeline is being built out in stages, based on how researchers actually use it.

It's real. It works. It will evolve, faster than qbase+ ever could, because we're the ones building it, and we're building it specifically for the researchers who've been left without a good option.

There is a free tier. It gives you access to the qPCR workflow and a set of standalone tools: geNorm, RDML viewer, and RDES validator. No credit card. No commitment. If something doesn't work the way you need it to, tell us. That feedback is genuinely how this gets better.