All pull requests

Pull requests

• Read pre-1.3.0 / CSV-only Xenium bundles

  #427·timtreis opened Oct 5, 2026Member·

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  13

• feat: Updates for 10x Genomics Atera bundles

  #426·stephenwilliams22 opened Sep 29, 2026Collaborator·

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  4

• Add experimental Pyxa (Stellaromics) reader

  #425·ckmah opened Sep 24, 2026Contributor·7 tasks done·

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  1

• Bump the actions-deps group across 1 directory with 7 updates

  dependenciesgithub_actions
  #424·dependabot[bot] opened Sep 22, 2026Bot·

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  1

• Adapt dega v2

  #423·cornhundred opened Sep 20, 2026·

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  1

• Respect filtered_counts_file when loading Visium HD cell matrices

  #421·psgundla opened Sep 14, 2026·

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  1

• Feat/xenium celldega regular grid

  #415·cornhundred opened Sep 6, 2026·

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  1

• Bump the pre-commit group across 1 directory with 4 updates

  dependenciespre_commit
  #412·dependabot[bot] opened Aug 11, 2026Bot·

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  1

• Support nf-core/mcmicro output in the mcmicro reader

  #410·adamjtaylor opened Jul 22, 2026·

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  1

  1

• feat: rewrite the CosMx reader (stitching, multimodal, co-registration)

  #406·timtreis opened Jun 28, 2026Member·

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• feat(xenium): import onboard secondary analysis (clustering/PCA/UMAP/diffexp) into the table

  #405·Tomatokeftes opened Jun 18, 2026·

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  2

• ci: bump codecov-action to v6 and fail CI on upload error

  #404·timtreis opened Jun 8, 2026Member·

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  1

• Testing cleanup

  #401·Darlokt opened May 16, 2026·

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  7

• New cosmx reader with stitching

  cosmx
  #339·quentinblampey opened Oct 31, 2025Contributor·

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