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CellMorphR v3.0.0

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@mbaffour mbaffour released this 24 Aug 14:57
· 7 commits to main since this release
v3.0.0
405fb92

Publication-ready figures, editable output, and hardened statistics.

Download and run

Grab CellMorphR-v3.0.0.zip, unzip it, and double-click:

OS Double-click
Windows run_cellmorphr.bat
macOS Run CellMorphR.command
Linux ./run.sh

The first run installs the required R packages (a few minutes); after that the app opens in your browser instantly. R must be installed: https://cran.r-project.org

What's new

Figures

  • SuperPlot options: shape-coded replicate dots, cells colored by biological replicate, per-group n on the axis - show sample-to-sample variation without needing p-values
  • Double-click any figure to edit its title, axis labels, legend title, caption, and condition names in place; renames apply across every tab, table, and export
  • Editable vector export: PDF, SVG, EPS, TIFF, PNG, plus PowerPoint (officer/rvg) where text and shapes stay editable, and a per-panel PPTX deck from the Pub Figure tab
  • Custom labels, fonts, sizes, colors, and point geometry on every plot tab

Statistics

  • Significance brackets now follow the test and correction chosen on the Statistics tab, so figures and tables always agree
  • 95% confidence intervals and degrees of freedom in the pairwise table
  • Small-n guardrails: the app warns when Wilcoxon cannot reach p<0.05 for the available replicate counts (n=2 vs 2 has a minimum attainable p of 0.33)
  • New dose-response trend test: fits replicate summaries against a numeric predictor per stratum with slope, 95% CI, p and R-squared
  • Split Condition labels such as pSJExD_gp75_100nM into vector and numeric dose columns for factorial and gradient designs
  • All hypothesis tests continue to run on biological-replicate summaries, never on individual cells

Layout and fixes

  • All 48 figure variants audited and fixed for overlapping text: wrapped titles, subtitles, captions and legend entries; stacked legends; brackets capped per timepoint; adaptive axis-label wrapping
  • Repaired plots that previously failed to build: Effect Sizes, the EMM plot, and the Cell Metrics heatmap
  • Fixes to log scales, bracket vs manual Y limits, EPS export without cairo, session restore, and PCA loading labels

See METHODS.md for a citable description of the plotting and statistics.

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