qPCR Tool Update!

· 2 min read · Discussion

qPCR Tool Update!

A while back, I shared a Shiny app I built that lets you analyze qPCR data in one click — computing ΔΔCt and fold changes and generating publication-style bar charts with statistical annotations (see A Simple qPCR Tool for details). I was genuinely surprised by how enthusiastically everyone tried it out — and the feedback you sent in was incredibly valuable. Thank you so much for the support! 🙏

Main Interface

Based on your suggestions, I've made a number of improvements. Here's what's new:

Statistical Method Improvements

Special thanks to @Emberwhirl for the thoughtful feedback on statistics!

  1. More appropriate test domain: The previous version performed statistical tests directly on fold change values, which violates the normality assumption of ANOVA. Version 2.0 now performs tests on ΔΔCt by default, with an additional option to run tests on ΔCt instead.
  2. Kruskal-Wallis post hoc testing: Added support for non-parametric post hoc comparisons after a Kruskal-Wallis test.
  3. Multiple testing correction: Added FDR correction (Benjamini-Hochberg), Holm correction, and other p-value adjustment methods.

Plot Improvements

  1. Added options to plot using ±ΔΔCt or ±ΔCt error bars.
  2. Added box plot, violin plot, and beeswarm plot options.
  3. The number of columns in multi-panel figures is now adjustable.

UI Improvements

  1. Switched to the cleaner, more modern "yeti" Bootstrap theme.
  2. Advanced settings have been moved into collapsible sections, making the interface much less cluttered.
  3. Added a Chinese UI option (the help section is still being updated 💦) — you can now toggle between Chinese and English in the upper-right corner.
  4. You can now double-click cells in the data preview table to edit or exclude outlier values. All data modifications are fully traceable.
  5. Added example datasets (both .xlsx and .csv formats) to the GitHub repository.

The updated version is live at https://apps.bioinfospace.com/qpcr-analysis/. If you experience slow loading or a temporary outage, it's likely due to high traffic — just wait a moment and refresh the page. (Note: refreshing the browser will clear any data you've already loaded.)

This tool is fully open-source — source code is available at https://github.com/mianaz/qpcr_tool (MIT License). The documentation also includes instructions for self-hosting with rsconnect.

As always, please try it out and send your feedback — it's what makes this tool better! 🎉

Originally posted on WeChat Official Account: bioinfo_studyroom

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