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Re:PR#58 - Add STACAS as new method component - #85

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rcannood merged 12 commits into
openproblems-bio:mainfrom
carmonalab:stacas
Aug 12, 2026
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Re:PR#58 - Add STACAS as new method component#85
rcannood merged 12 commits into
openproblems-bio:mainfrom
carmonalab:stacas

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@JGarnica22

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Describe your changes

Add some minor changes on STACAS method previously added in PR #58

  • Not using raw counts for Seurat object
  • Using top 2000 HVG from pre-processed files as anchors.features

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes
  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

@JGarnica22 JGarnica22 mentioned this pull request Oct 3, 2025
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@JGarnica22

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Hi, just checking in on this PR. Let me know if there’s anything I should update or clarify to help move it forward. Thanks!

@rcannood rcannood left a comment

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LGTM, thank you @JGarnica22 !

@rcannood
rcannood merged commit b9c2956 into openproblems-bio:main Aug 12, 2026
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rcannood added a commit that referenced this pull request Aug 12, 2026
* add method STACAS

* add method STACAS

* updata changelog

* Update: base_r container

Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com>

* Update: STACAS installation with depedencies, compatible with new R container baser_r:1

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

* fix: move STACAS comment below the kBET on New functionality section

* fix: remove boilerplate comments for better readability

* add: method_types configuration

* fix: do not load unneeded counts, and specificy anchor.features

---------
Co-authored-by: Josep Garnica <JGarnica22@users.noreply.github.com>
Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com>
Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>
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2 participants