Can I analyse Ct values without designing an assay first?

Yes. The analysis tabs accept pasted Ct data directly, and each one ships a real example dataset so the expected input shape is visible.

Does it rank reference genes?

Yes. Candidate reference genes are ranked by expression stability, which is what decides whether a normaliser is usable in a given experiment.

Amplify

qPCR Design

Design a qPCR assay against a region of an open sequence, then analyse the data that comes back from the instrument. Design and analysis sit in the same tool, so the assay a result belongs to is the assay you designed rather than a row you re-typed.

Open qPCR Design Open the qPCR & digital PCR sample

The real qPCR corpus: ΔΔCt (separate + same-tube), a standard curve, a significance table, Vandesompele 2002 geNorm in wide and long form, real amplification curves. Opens on the human GAPDH and MYC transcripts those experiments actually measure, plus a 72 bp miRNA precursor that walks Design right up to its length limit

What it does

01TaqMan primer and probe design over a selected region or a whole sequence
02Designed primers and probe written back onto the map as annotations
03Relative quantification by the delta-delta Ct method
04Amplification curve analysis, converting a curve to a Cq value
05Reference-gene stability ranking for normalisation
06Worked example datasets for each analysis tab, from published data rather than invented numbers

What it runs on

Primer thermodynamics come from the nearest-neighbour Tm engine in packages/ports; the analysis methods follow their published definitions. The panel runs on @ports/discover, @ports/eds, @ports/melt, @ports/qpcr, @ports/rdml, @ports/workflow.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Can I analyse Ct values without designing an assay first?: Yes. The analysis tabs accept pasted Ct data directly, and each one ships a real example dataset so the expected input shape is visible.
Does it rank reference genes?: Yes. Candidate reference genes are ranked by expression stability, which is what decides whether a normaliser is usable in a given experiment.

Also searched as

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