All pull requests

Pull requests

• Fix LoadXenium for standalone gene panels

  #10514·YoukaiFromAccounting opened Sep 18, 2026Contributor·

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• Report SCTransform variable features that could not be scaled

  #10513·longmanz opened Sep 18, 2026Contributor·

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• Drop the cells an SCT model records but its assay does not have

  #10512·longmanz opened Sep 18, 2026Contributor·

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• Fix QV filtering in ReadXenium

  #10507·YoukaiFromAccounting opened Sep 14, 2026Contributor·

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• Make RunPCA, RunUMAP and RunTSNE depend only on their seed

  #10503·BenjaminDEMAILLE opened Sep 10, 2026Contributor·

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• Make dimnames unique before building a Seurat object from an SCE

  #10501·BenjaminDEMAILLE opened Sep 2, 2026Contributor·

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• 4/4: Report where a matrix stands against the 2^31 limit

  #10497·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• 3/4: Convert on-disk assays when building a Seurat object from an SCE

  #10496·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• 2/4: Warn whenever an out-of-memory layer is loaded into memory

  #10495·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• 1/4: DelayedMatrix backend for layers past the dgCMatrix 2^31 limit

  #10494·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• Six fixes, including the FOV crash and the two failing tests on main (replaces six PRs)

  #10492·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• Say why these calls fail (replaces six PRs, plus vars.to.regress)

  #10491·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• Stop exporting the whole dataset to every worker, and fix ScaleData(split.by) ordering (replaces four PRs)

  #10490·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• Spatial reader fixes: Xenium, Akoya, Nanostring, Visium (replaces seven PRs)

  #10489·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• SCTransform and PrepSCTFindMarkers fixes (replaces six PRs)

  #10488·BenjaminDEMAILLE opened Sep 1, 2026Contributor·

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• Read HDF5 with rhdf5 instead of hdf5r

  #10467·BenjaminDEMAILLE opened Aug 31, 2026Contributor·

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• Leave cells without usable prediction scores unlabelled

  #10461·BenjaminDEMAILLE opened Aug 31, 2026Contributor·

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• Edits to CreateCategoryMatrix for colon groups

  #10399·mccormickceci opened May 22, 2026Contributor·5 of 12 tasks·

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• Fix issue #9104: the ICA Dim Reduc rowname issue

  #10395·cyrillustan opened May 21, 2026Contributor·

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• Avoid densifying matrix in ProjectCellEmbeddings

  #10337·assaron opened Mar 18, 2026Contributor·

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• fix issues with image orientation for curio-seeker data

  #10302·Liuy12 opened Feb 9, 2026Contributor·

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• Feature: Updates for Space Ranger 4.0

  #9978·stephenwilliams22 opened Jul 1, 2025Contributor·5 tasks·

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• add function readMM_fast

  #9731·freeseek opened Mar 6, 2025·

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• feature: updates for cellranger 9.0

  #9541·stephenwilliams22 opened Dec 10, 2024Contributor·

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• Added the functionality of scale.factor in NormalizeData being set to "median" of counts

  #9389·pranavm2109 opened Oct 11, 2024·

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