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Add tutorials covering SpatialData, SnapATAC2, pertpy, LIANA+, scirpy BCR and decoupler - #298

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Zethson merged 2 commits into
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add-tutorials-core-package-gaps
Sep 9, 2026
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Add tutorials covering SpatialData, SnapATAC2, pertpy, LIANA+, scirpy BCR and decoupler#298
Zethson merged 2 commits into
mainfrom
add-tutorials-core-package-gaps

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@Zethson Zethson commented Sep 9, 2026

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Summary

Adds 10 tutorials. Part of scverse/scverse.github.io#142.

  • SpatialData: Introduction to SpatialData (Data structures), Reading Xenium data (Spatial)
  • SnapATAC2: Standard scATAC-seq pipeline (ATAC-seq), Single-cell multiome analysis (Multimodal)
  • pertpy: distances, perturbation spaces, perturbation efficacy in pooled CRISPR screens (scRNA-seq)
  • LIANA+: Cell-cell communication (new category)
  • scirpy: B-cell receptor analysis (Adaptive immune cell receptor)
  • decoupler: Single-cell enrichment analysis (scRNA-seq)

Cell-cell communication is a new value in the primary_category enum, so schema.json and categories.yml change too. Multimodal was already defined but had no tutorials.

Authors are taken from each notebook's upstream commit history. Icons come from the ecosystem-packages registry, except LIANA+ (own repo logo, resized to 446x512) and decoupler/scirpy (icons already in this repo).

… BCR and decoupler

Three core packages had no presence on /learn at all: SpatialData, SnapATAC2
and pertpy. This adds an entry point for each, plus tutorials that fill gaps
inside packages that were already listed.

Adds a Cell-cell communication category, which had no coverage, and fills the
Multimodal category, which was defined but empty and therefore never rendered.
@Zethson
Zethson merged commit 70f2006 into main Sep 9, 2026
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@Zethson
Zethson deleted the add-tutorials-core-package-gaps branch September 9, 2026 16:15
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