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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed

- Colocalization heatmap text now explains that proteins are selected by mean abundance (up to 40 markers), globally across samples or within each cell type.
- The Cell recovery section now explains how to read the molecule rank plot.
- Experiment Summary labels now use "isotype control markers" consistently.

## [0.14.0] 2026-08-25
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6 changes: 6 additions & 0 deletions inst/quarto/workflows/amplicon_demux/quality_metrics.qmd
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Expand Up @@ -137,6 +137,12 @@ close_tabset()

#### Number of components

The molecule rank plot below ranks the components of a sample from the most to the fewest molecules. Cells appear as
the plateau of large components to the left, and the curve drops where cells give way to background components such as
debris. A sharp drop means that cells are well separated from background, while a gradual slope means that the two are
harder to tell apart. The dashed lines mark the minimum and maximum component size thresholds, and only components
between them are kept as cells.
Comment on lines +140 to +144

```{r}
#| label: qc_metrics_molrank_plot
#| results: 'asis'
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