Issues

• Namespace cell IDs through one remap generic across gmulti subobjects

  giotto-suite/GiottoClass#440 · Filter by author jiajic opened on Sep 28, 2026

• Move low-level matrix primitives (allMatrix, thresholdParam, feat/cellStatsParam) down from Giotto

  giotto-suite/GiottoClass#427 · Filter by author jiajic opened on Sep 23, 2026

• Collapse materialize() and resolveSubobject() into one resolve() generic, and hand leaves their context instead of the gobject

  giotto-suite/GiottoClass#425 · Filter by author jiajic opened on Sep 22, 2026
  1

• materialize(): surviving-ID set is computed once against the active spat_unit, and ... is a dead end

  giotto-suite/GiottoClass#424 · Filter by author jiajic opened on Sep 22, 2026
  1

• saveGiotto() cannot save an in-memory giottoMulti

  giotto-suite/GiottoClass#407 · Filter by author jiajic opened on Sep 16, 2026

• Dead slots: networkParam@param, and spatialNetworkObj@outputObj

  giotto-suite/GiottoClass#405 · Filter by author jiajic opened on Sep 14, 2026

• Network wrappers expose a smaller argument surface than the params they build

  giotto-suite/GiottoClass#404 · Filter by author jiajic opened on Sep 14, 2026

• nnData and spatNetData share no network parent, so every network method is written twice

  giotto-suite/GiottoClass#403 · Filter by author jiajic opened on Sep 14, 2026

• maximum_distance on kNNNetworkParam is accepted and never read unless filter = TRUE

  giotto-suite/GiottoClass#402 · Filter by author jiajic opened on Sep 14, 2026

• networkParam hierarchy: shared slots are duplicated and domain is carried by a method default

  giotto-suite/GiottoClass#401 · Filter by author jiajic opened on Sep 14, 2026
  2

• Clustering Error in Giotto 3.3.2: “object of type ‘S4’ is not subsettable” While Running doLeidenCluster

  giotto-suite/GiottoClass#379 · Filter by author TATABOX99 opened on Jun 27, 2026

• Remove spatVectorCentroids slot from giottoPolygon

  giotto-suite/GiottoClass#342 · Filter by author jiajic opened on Apr 15, 2026

• track multiply order in affine object

  Feature

  giotto-suite/GiottoClass#340 · Filter by author jiajic opened on Jan 28, 2026

• subsetGiotto error

  giotto-suite/GiottoClass#329 · Filter by author YinCY123 opened on Oct 22, 2025

• anndataToGiotto fails to load from H5AD

  giotto-suite/GiottoClass#319 · Filter by author xw363 opened on Jul 8, 2025

• seuratToGiotto5 doesn't work

  giotto-suite/GiottoClass#316 · Filter by author marijazmf opened on Jul 7, 2025
  7

• Improve handling of python path setting errors

  documentation
  giotto-suite/GiottoClass#284 · Filter by author jiajic opened on Feb 26, 2025

• Metaobject for joining heterogeneous data

  enhancement
  giotto-suite/GiottoClass#260 · Filter by author jiajic opened on Dec 16, 2024

• calculateOverlap on aligned image fails to capture overlaps

  bug
  giotto-suite/GiottoClass#259 · Filter by author kunleng opened on Dec 11, 2024
  4

• Misinformation when using anndataToGiotto with non default env_name

  documentation
  giotto-suite/GiottoClass#230 · Filter by author wwang-chcn opened on Aug 29, 2024
  5

• Replacement functions for spatial and feature IDs

  enhancement
  giotto-suite/GiottoClass#226 · Filter by author jiajic opened on Aug 28, 2024

• Allow repository selection in installGiottoEnvironment()

  enhancement
  giotto-suite/GiottoClass#224 · Filter by author jiajic opened on Aug 28, 2024