All pull requests

Pull requests

• Document CellTypist cell type prediction

  #391·mumichae with CopilotAI opened Oct 5, 2026·

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• integration: add Seurat v5 RPCA method (seurat_rpca)

  #390·mtd91429 opened Oct 4, 2026Contributor·

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• integration/drvi: set the random seed

  #389·mtd91429 opened Oct 4, 2026Contributor·

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• integration/sysvi: pass early_stopping on to model.train

  #388·mtd91429 opened Oct 4, 2026Contributor·

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• doublets/collect: read only the slots that an h5ad input has

  #387·mtd91429 opened Oct 4, 2026Contributor·

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• Scanorama integration fixes

  #386·mtd91429 opened Oct 3, 2026Contributor·

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• Drop cell_passed_qc column

  #385·Arkkienkeli opened Oct 1, 2026·

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• Fix HB regex

  #384·Arkkienkeli opened Oct 1, 2026·

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• Clean up Preprocessing Module

  #382·seohyonkim opened Jul 13, 2026Collaborator·

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• remove hard-coded gpu calls

  #381·jn-goe opened Jun 30, 2026·

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• draft: improve quickstart pipeline just so that it works..

  #380·seohyonkim opened Jun 29, 2026Collaborator·

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• QC modularisation (stand-alone and snakemake compatible)

  #379·cramsuig opened Jun 16, 2026Collaborator·

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• metrics: use .toarray() to avoid np.matrix from .todense()

  #378·mtd91429 opened Jun 14, 2026Contributor·

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• Score_genes has undefined logger + duplicate-feature var mask

  #377·mtd91429 opened Jun 14, 2026Contributor·

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• Fix scanpy_to_neighborsresults neighbor convention

  #376·mtd91429 opened Jun 14, 2026Contributor·

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• Fix ari_kmeans_y and nmi_kmeans_y

  #375·mtd91429 opened Jun 14, 2026Contributor·

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• Handle empty .var from integration outputs in metrics prepare

  #374·mtd91429 opened Jun 14, 2026Contributor·

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• Add module documentation for marker_genes

  #373·mumichae with CopilotAI opened Jun 4, 2026·

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• pcr_y: use precomputed obsm['X_pca'] instead of raw .X

  #371·mtd91429 opened May 22, 2026Contributor·

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• Load data: schema_file optional

  #363·mumichae opened Apr 2, 2026Member·

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• Reference mapping: SCimilarity

  #357·mumichae opened Mar 15, 2026Member·

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• Add harmonypy adapted LISI functions

  #133·mumichae opened Mar 20, 2024Member·

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