v1.2.0

Added

• Stability of reference genes: geNorm M with stepwise exclusion and pairwise variation V, NormFinder ρ with sample groups and the best pair of genes. Checked against NormqPCR and ctrlGene on their published data sets.
• A Stability page: candidate genes with check boxes, the advice on how many references to take and which, a button that makes them the references; geNorm and NormFinder figures.
• QC: a warning when a chosen reference is not stable in the experiment (geNorm M above a limit set in the analysis settings), a note for a single reference, a note for samples left out of the ranking.
• A Stability sheet in the workbook, a section in the HTML report, the stability figures in exported figures and qpcrkit analyze --figures.
• A warning when a well has two reactions with the same target and dye; only the first is used.

Changed

• When the analysis fails, the result pages say so instead of showing the previous results.

Fixed

• A target name starting with "_" no longer disappears from the legend of curve figures.
• The curve graph keeps its saved picture when its size does not change.

v1.1.0

Added

• A new workspace: navigation with the runs on the left, reference and control chips on top, a hint line that says what is missing next, a start screen with drag and drop and a demo project.
• Curve analysis: baseline, Cq at a common threshold, per-well efficiency in a window of linearity, melt peaks and Tm, compared with instrument results on real files. The instrument's Cq stays the default; Cq and efficiency from curves are an explicit choice.
• The curve graph beside the plate and linked with it, a threshold line that can be dragged, per-run manual thresholds with an Auto button.
• New QC from curves: several melt peaks, Tm shift, a product or dimers in the NTC, disagreement with the instrument's Cq, very early Cq, Cq without amplification, mixed Cq sources, thresholds that differ without calibrators.
• Exclude a standard by clicking its point; save the expression figure from its page; curve columns in the data table, a Curves sheet in the workbook, curve figures in the HTML report and in the exported figures; qpcrkit analyze --cq-source.
• QuantStudio Design & Analysis workbooks; RDML 1.0 and 1.1; several CFX files or a whole folder as one run.
• Amplification and melt curves are imported and stored in the project.
• Assign targets to wells, rename a target on a plate, name samples in series, paste a plate map from a spreadsheet.
• No-RT control role (nrt) with its own check.
• Reference genes and calibrator named by the file are offered after import.

Changed

• A calm theme with a teal accent and line icons; analysis settings moved to a dialog, reference and control to the top bar.
• Project files are smaller: curves of a run share one axis.
• The theme follows the system by default; light and dark can still be chosen.
• Wells without a sample are no longer treated as replicates of each other.

Fixed

• Checked boxes show a tick; lists and spin boxes show their arrows.
• Numbers are read by column: 1,250.000 and 100,000,000 no longer lose standard quantities, and a Russian dilution series keeps its decimals.
• Binary instrument files give a clear message.
• QC messages show the thresholds from the settings.
• Command line: a missing file, a locked xlsx or an unknown --ref/--control give a message instead of a traceback.
• Target names cannot break figure file names; the standards tab keeps the selected curve.
• A wrong quantity is refused instead of breaking the standard curve.

v1.0.0

Full Changelog: https://github.com/adrobi/qpcrkit/commits/v1.0.0