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ewels merged 2 commits into from
Feb 14, 2026
Merged

Fix image paths and add dupRadar benchmark comparisons #15

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0540849
fix: use dynamic base URL for doc images and add featurecounts benchm…
claude Feb 14, 2026
590c840
fix: use dynamic base URL for benchmark page images
claude Feb 14, 2026
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32 changes: 17 additions & 15 deletions docs/src/content/docs/benchmarks/dupradar.md → .../src/content/docs/benchmarks/dupradar.mdx
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Expand Up @@ -3,6 +3,8 @@ title: dupRadar Benchmark
description: Performance comparison between RustQC and R dupRadar, with zero output mismatches across all values.
---

export const base = import.meta.env.BASE_URL;

RustQC produces output **identical** to the R dupRadar package. Every value in the duplication matrix, every count, and the fitted model parameters match exactly. The benchmarks below quantify the performance difference on real RNA-seq data.

## Small benchmark
Expand Down Expand Up @@ -69,39 +71,39 @@ The plots below compare the R dupRadar output (left) with RustQC output (right)

#### Density scatter plot

<div style="display: grid; grid-template-columns: 1fr 1fr; gap: 1rem; margin: 1rem 0;">
<figure style="margin: 0; text-align: center;">
<img src="/benchmarks/large/dupRadar/duprateExpDens.png" alt="dupRadar (R) density scatter plot" style="width: 100%;" />
<div style={{display: "grid", gridTemplateColumns: "1fr 1fr", gap: "1rem", margin: "1rem 0"}}>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/dupRadar/duprateExpDens.png`} alt="dupRadar (R) density scatter plot" style={{width: "100%"}} />
<figcaption>dupRadar (R)</figcaption>
</figure>
<figure style="margin: 0; text-align: center;">
<img src="/benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_duprateExpDens.png" alt="RustQC density scatter plot" style="width: 100%;" />
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_duprateExpDens.png`} alt="RustQC density scatter plot" style={{width: "100%"}} />
<figcaption>RustQC</figcaption>
</figure>
</div>

#### Duplication rate boxplot

<div style="display: grid; grid-template-columns: 1fr 1fr; gap: 1rem; margin: 1rem 0;">
<figure style="margin: 0; text-align: center;">
<img src="/benchmarks/large/dupRadar/duprateExpBoxplot.png" alt="dupRadar (R) duplication rate boxplot" style="width: 100%;" />
<div style={{display: "grid", gridTemplateColumns: "1fr 1fr", gap: "1rem", margin: "1rem 0"}}>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/dupRadar/duprateExpBoxplot.png`} alt="dupRadar (R) duplication rate boxplot" style={{width: "100%"}} />
<figcaption>dupRadar (R)</figcaption>
</figure>
<figure style="margin: 0; text-align: center;">
<img src="/benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_duprateExpBoxplot.png" alt="RustQC duplication rate boxplot" style="width: 100%;" />
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_duprateExpBoxplot.png`} alt="RustQC duplication rate boxplot" style={{width: "100%"}} />
<figcaption>RustQC</figcaption>
</figure>
</div>

#### Expression histogram

<div style="display: grid; grid-template-columns: 1fr 1fr; gap: 1rem; margin: 1rem 0;">
<figure style="margin: 0; text-align: center;">
<img src="/benchmarks/large/dupRadar/expressionHist.png" alt="dupRadar (R) expression histogram" style="width: 100%;" />
<div style={{display: "grid", gridTemplateColumns: "1fr 1fr", gap: "1rem", margin: "1rem 0"}}>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/dupRadar/expressionHist.png`} alt="dupRadar (R) expression histogram" style={{width: "100%"}} />
<figcaption>dupRadar (R)</figcaption>
</figure>
<figure style="margin: 0; text-align: center;">
<img src="/benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_expressionHist.png" alt="RustQC expression histogram" style="width: 100%;" />
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_expressionHist.png`} alt="RustQC expression histogram" style={{width: "100%"}} />
<figcaption>RustQC</figcaption>
</figure>
</div>
Expand Down
45 changes: 45 additions & 0 deletions .../content/docs/benchmarks/featurecounts.md → ...content/docs/benchmarks/featurecounts.mdx
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Expand Up @@ -3,6 +3,8 @@ title: featureCounts Benchmark
description: Performance and accuracy comparison between RustQC's built-in read counting and Rsubread featureCounts.
---

export const base = import.meta.env.BASE_URL;

RustQC includes built-in gene-level read counting that produces output
compatible with the Subread featureCounts format. This page compares the
counting performance and output accuracy against standalone Rsubread
Expand Down Expand Up @@ -48,6 +50,49 @@ exactly.
The output format is directly compatible with downstream tools such as DESeq2
and MultiQC.

### Side-by-side plots

Since dupRadar visualizations are derived from the same gene-level counts, identical plots confirm that the underlying feature counting is correct. The plots below compare R dupRadar output (left) with RustQC output (right) for the large benchmark.

#### Density scatter plot

<div style={{display: "grid", gridTemplateColumns: "1fr 1fr", gap: "1rem", margin: "1rem 0"}}>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/dupRadar/duprateExpDens.png`} alt="dupRadar (R) density scatter plot" style={{width: "100%"}} />
<figcaption>dupRadar (R)</figcaption>
</figure>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_duprateExpDens.png`} alt="RustQC density scatter plot" style={{width: "100%"}} />
<figcaption>RustQC</figcaption>
</figure>
</div>

#### Duplication rate boxplot

<div style={{display: "grid", gridTemplateColumns: "1fr 1fr", gap: "1rem", margin: "1rem 0"}}>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/dupRadar/duprateExpBoxplot.png`} alt="dupRadar (R) duplication rate boxplot" style={{width: "100%"}} />
<figcaption>dupRadar (R)</figcaption>
</figure>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_duprateExpBoxplot.png`} alt="RustQC duplication rate boxplot" style={{width: "100%"}} />
<figcaption>RustQC</figcaption>
</figure>
</div>

#### Expression histogram

<div style={{display: "grid", gridTemplateColumns: "1fr 1fr", gap: "1rem", margin: "1rem 0"}}>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/dupRadar/expressionHist.png`} alt="dupRadar (R) expression histogram" style={{width: "100%"}} />
<figcaption>dupRadar (R)</figcaption>
</figure>
<figure style={{margin: 0, textAlign: "center"}}>
<img src={`${base}benchmarks/large/RustQC/GM12878_REP1.markdup.sorted_expressionHist.png`} alt="RustQC expression histogram" style={{width: "100%"}} />
<figcaption>RustQC</figcaption>
</figure>
</div>

## Additional outputs

Beyond the standard featureCounts counts file and summary, RustQC also
Expand Down
8 changes: 5 additions & 3 deletions docs/src/content/docs/outputs/dupradar.mdx
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Expand Up @@ -5,6 +5,8 @@ description: Comprehensive guide to RustQC's dupRadar output files, including th

import { Card, CardGrid, FileTree } from '@astrojs/starlight/components';

export const base = import.meta.env.BASE_URL;

## What is dupRadar?

In DNA sequencing, PCR duplicates are straightforward to identify and remove: reads with identical alignment coordinates are likely amplification artifacts. In **RNA-seq**, the situation is more nuanced.
Expand Down Expand Up @@ -118,15 +120,15 @@ See the [Interpreting plots](#interpreting-plots) section below for how to read
<CardGrid>
<Card title="Density scatter plot">
`<sample>_duprateExpDens.{png,svg}`
![Density scatter plot](/RustQC/examples/dupradar/duprateExpDens.png)
<img src={`${base}examples/dupradar/duprateExpDens.png`} alt="Density scatter plot" />
</Card>
<Card title="Duplication rate boxplot">
`<sample>_duprateExpBoxplot.{png,svg}`
![Duplication rate boxplot](/RustQC/examples/dupradar/duprateExpBoxplot.png)
<img src={`${base}examples/dupradar/duprateExpBoxplot.png`} alt="Duplication rate boxplot" />
</Card>
<Card title="Expression histogram">
`<sample>_expressionHist.{png,svg}`
![Expression histogram](/RustQC/examples/dupradar/expressionHist.png)
<img src={`${base}examples/dupradar/expressionHist.png`} alt="Expression histogram" />
</Card>
</CardGrid>

Expand Down
12 changes: 7 additions & 5 deletions docs/src/content/docs/outputs/rseqc.mdx
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Expand Up @@ -5,6 +5,8 @@ description: Output files produced by RustQC's RSeQC-compatible quality control

import { Card, CardGrid, FileTree } from '@astrojs/starlight/components';

export const base = import.meta.env.BASE_URL;

RustQC reimplements seven tools from the [RSeQC](https://rseqc.sourceforge.net/)
package. Each tool produces output files that match the format and content of the
original Python implementation, plus **native PNG and SVG plots** generated
Expand Down Expand Up @@ -87,7 +89,7 @@ high duplication.

<CardGrid>
<Card title="Duplication rate">
<img src="/RustQC/examples/rseqc/read_duplication.png" alt="Read duplication rate plot" />
<img src={`${base}examples/rseqc/read_duplication.png`} alt="Read duplication rate plot" />
</Card>
</CardGrid>

Expand Down Expand Up @@ -136,10 +138,10 @@ known (blue), partial novel (red), and complete novel (green) splicing.

<CardGrid>
<Card title="Splice events">
<img src="/RustQC/examples/rseqc/splice_events.png" alt="Splice events pie chart" />
<img src={`${base}examples/rseqc/splice_events.png`} alt="Splice events pie chart" />
</Card>
<Card title="Splice junctions">
<img src="/RustQC/examples/rseqc/splice_junction.png" alt="Splice junctions pie chart" />
<img src={`${base}examples/rseqc/splice_junction.png`} alt="Splice junctions pie chart" />
</Card>
</CardGrid>

Expand Down Expand Up @@ -169,7 +171,7 @@ detected (in thousands). A plateau in the curves indicates saturation.

<CardGrid>
<Card title="Junction saturation">
<img src="/RustQC/examples/rseqc/junction_saturation.png" alt="Junction saturation plot" />
<img src={`${base}examples/rseqc/junction_saturation.png`} alt="Junction saturation plot" />
</Card>
</CardGrid>

Expand Down Expand Up @@ -210,7 +212,7 @@ approximately normal for a well-prepared library.

<CardGrid>
<Card title="Inner distance">
<img src="/RustQC/examples/rseqc/inner_distance.png" alt="Inner distance histogram" />
<img src={`${base}examples/rseqc/inner_distance.png`} alt="Inner distance histogram" />
</Card>
</CardGrid>

Expand Down
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