Issues

• Let unlink name the assays to unlink in setSubsetExperiment() and setSubsetAssay()

  enhancement
  campbio/ExperimentSubset#59 · Filter by author joshua-d-campbell opened on Oct 27, 2026

• A subset can't see the main object's altExps

  enhancement
  campbio/ExperimentSubset#58 · Filter by author joshua-d-campbell opened on Oct 27, 2026

• colData(x, subsetName =, parentColData = TRUE) returns duplicate column names, and $ reads the main object's copy

  bug
  campbio/ExperimentSubset#57 · Filter by author joshua-d-campbell opened on Oct 27, 2026

• Optional BiocCheck NOTEs: R dependency, biocViews, vignette chunk labels

  documentation
  campbio/ExperimentSubset#52 · Filter by author joshua-d-campbell opened on Oct 23, 2026

• Design: let subset rowData/colData inherit down the subset tree (parentColData/parentRowData stay)

  enhancementquestion
  campbio/ExperimentSubset#50 · Filter by author joshua-d-campbell opened on Oct 23, 2026
  1

• subsetRowLinks/subsetColLinks/subsetSpatialData return rownames "1".."n" instead of the subset's names

  bug
  campbio/ExperimentSubset#47 · Filter by author joshua-d-campbell opened on Oct 22, 2026

• Writing back colData(x, subsetName =, parentColData = TRUE) duplicates the parent columns

  bug
  campbio/ExperimentSubset#46 · Filter by author joshua-d-campbell opened on Oct 22, 2026

• subsetColLinks(x, s, parentColLinkData = TRUE) errors on a TreeSE without a column tree

  bug
  campbio/ExperimentSubset#44 · Filter by author joshua-d-campbell opened on Oct 22, 2026

• reducedDim(es, subsetName = ) without type errors instead of returning the first reducedDim

  bug
  campbio/ExperimentSubset#39 · Filter by author joshua-d-campbell opened on Oct 22, 2026

• Lint backlog: 908 findings from make lint

  enhancement
  campbio/ExperimentSubset#37 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Reduce duplicated method code across the five Subset<Class>.R files

  enhancement
  campbio/ExperimentSubset#36 · Filter by author joshua-d-campbell opened on Oct 21, 2026
  1

• TreeSummarizedExperiment subset support is incomplete (rowLinks/colLinks, rowTree/colTree)

  enhancement
  campbio/ExperimentSubset#35 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• subsetSpatialData relies on SpatialExperiment's deprecated spatialData()

  enhancement
  campbio/ExperimentSubset#34 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Roxygen, DESCRIPTION, CITATION and README fixes

  documentation
  campbio/ExperimentSubset#33 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Vignette inaccuracies: supported classes, createSubset argument names, unseeded random data

  documentation
  campbio/ExperimentSubset#32 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Strengthen weak test assertions and clean up the test file

  enhancement
  campbio/ExperimentSubset#31 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• No tests for TreeSummarizedExperiment or SpatialExperiment; test suite downloads pbmc4k

  enhancement
  campbio/ExperimentSubset#30 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• rowData<-/colData<- with a non-DataFrame value may bypass subsetName; withDimnames and use.names are dropped

  bug
  campbio/ExperimentSubset#29 · Filter by author joshua-d-campbell opened on Oct 21, 2026
  3

• subsetParent() can loop forever when a subset-assay name is reused

  bug
  campbio/ExperimentSubset#28 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Input validation gaps: indices, subset names, constructor subset=, unknown subset names

  bug
  campbio/ExperimentSubset#27 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Package reducedDims<- and reducedDimNames generics mask SingleCellExperiment's (needs discussion)

  bugquestion
  campbio/ExperimentSubset#26 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Subset names with spaces are stripped in the object but stored under the original key

  bug
  campbio/ExperimentSubset#25 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• setSubsetAssay overwrites the subset's dimnames with the input matrix's

  bug
  campbio/ExperimentSubset#24 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• Subsets with one row or column return a vector (missing drop = FALSE)

  bug
  campbio/ExperimentSubset#23 · Filter by author joshua-d-campbell opened on Oct 21, 2026

• callNextMethod(...) drops x when extra arguments are passed, so reducedDim(es, 'PCA', withDimnames = FALSE) errors

  bug
  campbio/ExperimentSubset#22 · Filter by author joshua-d-campbell opened on Oct 21, 2026