Skip to content

CLAUDE.md

Latest commit

 

History

History
27 lines (16 loc) · 1.28 KB

CLAUDE.md

File metadata and controls

27 lines (16 loc) · 1.28 KB

CLAUDE.md

Read-only Shiny app viewer for Seurat v4 and v5 objects.

Core Constraints

  • Do NOT add analysis functions, data transformations, or object modifications.
  • Use LayerData(obj, layer = "counts") for data access, not direct slot access

Seurat/Bioinformatics

  • SCTAssay does NOT have a @layers slot — direct @layers[["..."]] access crashes on it.
  • Use get_layer_dim(assay_obj, layer) in seurat_utils.R to safely get per-layer dimensions; it checks slotNames first and falls back appropriately. Same pattern applies anywhere you need to touch a layer's underlying matrix on an arbitrary assay type.
  • Seurat uses specialized assay classes: ChromatinAssay (Signac) for ATAC, SCTAssay for SCT
  • VisiumV2 is a subclass of FOV; VisiumV1 is NOT (it extends SpatialImage directly) — always check both classes explicitly

Shiny/CSS Gotcha

AdminLTE has deep CSS specificity — CSS overrides must target actual shinydashboard DOM structure with browser-inspector-level selectors.

Critical: Namespace Prefixes

ALWAYS use explicit namespace prefixes (SeuratObject::Layers(), shiny::renderUI(), DT::datatable()). The app.R launcher sources R/ files directly, bypassing NAMESPACE.

Sundry

  • Keep settings.local.json in .claude/ directory (not project root).