Interactive Marker-Gene Explorer

This interactive companion to the Cell-Type Annotation and Differential Expression episode lets you explore the cluster markers we compute with FindAllMarkers.

Click any cluster on the Harmony UMAP (or use the dropdown) to see the genes that distinguish it from all other nuclei — gene symbol, NCBI product description, and the FindAllMarkers statistics (avg_log2FC, pct.1, pct.2, and the adjusted p-value). The table is sorted by effect size and is searchable, so you can defend a cluster’s identity from its top markers.

Note

The app runs entirely in your browser (no server). The first load downloads the R runtime and may take 10–20 seconds — give it a moment to start.

---
title: "Interactive Marker-Gene Explorer"
page-layout: full
toc: false
---

This interactive companion to the [Cell-Type Annotation and Differential
Expression](snrnaseq-annotation-and-de.html) episode lets you explore the
cluster markers we compute with `FindAllMarkers`.

**Click any cluster** on the Harmony UMAP (or use the dropdown) to see the genes
that distinguish it from all other nuclei — gene symbol, NCBI product
description, and the `FindAllMarkers` statistics (`avg_log2FC`, `pct.1`, `pct.2`,
and the adjusted *p*-value). The table is sorted by effect size and is
searchable, so you can defend a cluster's identity from its top markers.

::: {.callout-note}
The app runs entirely in your browser (no server). The first load downloads the
R runtime and may take 10–20 seconds — give it a moment to start.
:::

::: {.column-screen-inset-right}
```{=html}
<iframe src="https://d18e7eu8nurr5a.cloudfront.net/apps/marker-explorer/index.html"
        title="EO Marker-Gene Explorer"
        style="width:100%; height:85vh; min-height:640px; border:1px solid #ddd; border-radius:6px;"
        loading="lazy"
        allow="cross-origin-isolated">
</iframe>
```
:::