NEWS
CellMentor 1.1.2 (2026-05-22)
Bug fixes
calculate_performance() now passes as.factor(true_labels) and
as.factor(clusters) to aricode::NMI(). As of aricode 1.1.0
(currently shipping in Bioconductor 3.24), NMI() routes mixed-type
inputs through sort_pairs(), which calls as.integer() on character
labels — turning cell-type names such as "alpha" into NA and aborting
with "NA are not supported.". Coercing both sides to factor keeps the
computation well-defined and restores compatibility with the Bioconductor
build farm. This was the underlying cause of the vignette failure that
1.1.1 surfaced but did not fix.
CellMentor 1.1.1 (2026-05-19)
Bug fixes
cluster_nmf() now falls back to k-means clustering when the NMF
embedding has too few features or cells for SNN (variable-feature
selection on low-dim embeddings was failing under Seurat 5.x). The
number of k-means / hclust centers is now clamped to a feasible range,
so grid search no longer fails silently on small reference splits.
CellMentor() now stops with a clear message if every parameter
configuration in the grid search fails, instead of cascading to a
cryptic switch() error during final-model training.
evaluate_params() warnings now include the underlying error message,
so build logs surface the real cause of failures.
initialize_wh() validates that method is a single character string
and reports a helpful error if not.
Documentation
- Updated citation to the published Nature Communications paper
(Hevdeli et al., 2026, doi:10.1038/s41467-025-67088-7).
- Added
inst/CITATION so citation("CellMentor") returns a structured
bibliographic entry.
CellMentor 0.99.2 (2024-12-10)
CHANGES FOR BIOCONDUCTOR REVIEW
- Replaced
parallel package with BiocParallel for Bioconductor compliance
- Renamed
h.baron_dataset() to hBaronDataset() (old name deprecated)
- Updated R version requirement to >= 4.5.0
- Removed
GeneExpression from biocViews (redundant with Transcriptomics)
CellMentor 0.99.1 (2024-10-27)
- Initial Bioconductor submission of CellMentor.