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feat: subtype tree documentation and release notes#172

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mkirk111 merged 20 commits into
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subtype_tree_2026_5
May 20, 2026
Merged

feat: subtype tree documentation and release notes#172
mkirk111 merged 20 commits into
mainfrom
subtype_tree_2026_5

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This pull request updates the PeCan documentation to introduce and describe the new Subtype Tree feature, which enhances navigation and exploration of pediatric cancer diagnoses using the CC4K framework. The changes also improve the clarity and structure of the Diagnosis Search section and update the release notes to reflect the latest features.

New Subtype Tree Feature and Documentation Updates:

  • Added a new section in the documentation describing the Subtype Tree, which provides a hierarchical, navigable view of pediatric cancer diagnoses, allows node expansion to reveal subtypes, displays sample counts, includes node tooltips, and supports SVG download.
  • Updated the Diagnosis Search section to clarify the distinction and relationship between the Sunburst and Subtype Tree tools, and improved explanations of their navigation and data exploration capabilities.

Release Notes Enhancements:

  • Added a May 2026 entry to the release notes, highlighting the introduction of the Subtype Tree, node tooltips, and download options for both the tree and metadata.

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Pull request overview

This PR updates the PeCan documentation to introduce the new Subtype Tree feature, clarify how it relates to the existing Sunburst-based Diagnosis Search experience, and adds a May 2026 entry to the PeCan release notes.

Changes:

  • Added May 2026 release notes describing the Subtype Tree feature and related capabilities.
  • Restructured the “Diagnosis Search” documentation to describe both Sunburst and Subtype Tree, including navigation/download behavior.
  • Updated dataset documentation formatting/anchors and expanded the spellcheck allowlist for newly introduced domain terms.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 9 comments.

File Description
content/4.pecan/5.release-notes/1.index.md Adds May 2026 release notes and adjusts Feb 2026 formatting.
content/4.pecan/1.overview/1.getting-started.md Expands/clarifies Diagnosis Search docs and adds a new Subtype Tree section.
content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md Fixes anchors/table formatting and updates dataset text.
.spelling Adds new domain terms to pass markdown-spellcheck.
Comments suppressed due to low confidence (2)

content/4.pecan/5.release-notes/1.index.md:34

  • The follow-up sentences for the “Redesigned Navigation” and “Help Guides” bullets are not indented, so Markdown will break the list and render them as separate paragraphs. Indent those wrapped lines so they remain part of their respective bullet items.
- **Redesigned Navigation:** New left-side navigation panel for easy navigation between data facets and access to the [Diagnosis Search](../../2.cc4k/1.index.md).
This redesign lays the groundwork for a new cohort building feature that we expect to land later this year—stay tuned!
- **Help Guides:** Navigation to our PeCan Help Guide documentation is now accessible on the new left-side navigation panel.
We intend to continue contributing heavily to PeCan's help guides in the months and years to come.

content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md:181

  • The DAU acronym “PCPG” appears in this table, but the DAU is defined above as “PCGP” (Pediatric Cancer Genome Project). Please correct “PCPG” to “PCGP” in these affected rows to keep DAU names consistent.
| [PBTP](#pediatric-brain-tumor-program)                                                           | PCPG, Clinical Genomics | —                   | WES, WGS, RNA-Seq         |      97 |
| [PCGP](#pediatric-cancer-genome-project)                                                         | PCGP                    | Paired Tumor-Normal | WGS, WES, RNA-Seq         |   3,031 |
| [PedAML](#pediatric-acute-myeloid-leukemia-pedaml)                                               | PCGP                    | —                   | WES, WGS, RNA-Seq         |     275 |
| [RPAML](#genomics-and-transcriptomics-of-relapsed-pediatric-aml-rpaml)                           | PCPG, Clinical Genomics | —                   | WGS, RNA-Seq              |     265 |
| [RTCG](#real-time-clinical-genomics)                                                             | PCPG, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq         |   2,371 |

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Comment thread content/4.pecan/1.overview/1.getting-started.md Outdated
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Looks good. One question on if we want a link but not a blocker.

Comment thread content/4.pecan/1.overview/1.getting-started.md
mkirk111 and others added 8 commits May 20, 2026 10:23
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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Pull request overview

Copilot reviewed 4 out of 5 changed files in this pull request and generated 4 comments.

Comment thread content/4.pecan/5.release-notes/1.index.md
Comment thread content/4.pecan/5.release-notes/1.index.md Outdated
Comment thread content/4.pecan/1.overview/1.getting-started.md Outdated
Comment thread .spelling Outdated
mkirk111 and others added 3 commits May 20, 2026 13:04
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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Still looks good after moving a second sentence to a new line and then fixing the spellcheck.

Comment thread content/4.pecan/5.release-notes/1.index.md Outdated
@mkirk111 mkirk111 merged commit 9a7fd9c into main May 20, 2026
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@mkirk111 mkirk111 deleted the subtype_tree_2026_5 branch May 20, 2026 21:41
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3 participants