NEWS

multipletR 0.99.9

Added @importClassesFrom SingleCellExperiment SingleCellExperiment so the imported class is used by the object-type check, resolving the "declared Import not used" note while keeping SingleCellExperiment in Imports.

Kept SingleCellExperiment in Imports (the package supports SCE objects); removed the unused importFrom so the package builds cleanly.

Moved SingleCellExperiment to Suggests and removed its unused importFrom (the class is checked via methods::is(), so the package is not needed at load time). Fixes the build failure from 0.99.6.

Moved SummarizedExperiment from Imports to Suggests (only used in tests).
Vignette: added an install chunk for the optional Seurat/SingleCellExperiment dependencies and removed the requireNamespace() guards and print() calls from the example chunks.

Vignette: the Seurat and SingleCellExperiment examples now run (removed eval = FALSE), using a small self-contained toy object, and show that the two object types give an identical classification. Also noted Seurat::as.SingleCellExperiment() for conversion.
remove_multiplets(): simplified the metadata-writing code using the x$<name> accessor, which works for both Seurat and SingleCellExperiment.
Started tracking changes in this NEWS file.

Removed the placeholder inst/CITATION file, since Bioconductor guidance is to include a CITATION only when there is an associated preprint or publication (will be restored with a DOI once published).
Added the Classification biocView and expanded the package Description.

remove_multiplets(): renamed from remove_multiplets_seurat(); now auto-detects whether the input is a Seurat or SingleCellExperiment object instead of requiring an object argument.
remove_multiplets(): remove = FALSE is now the default (annotate only); added a verbose argument and argument validation.
detect_multiplets(): added a verbose argument gating progress messages.
Added a package-level help page (?multipletR).
Vignette: switched to BiocStyle::html_document, added package hyperlinks (CRANpkg()/Biocpkg()/Githubpkg()), and added author/date.
Updated installation instructions to use BiocManager::install().
Added the fnd role and funding information to Authors@R.
Added unit tests for the plotting functions.

Initial Bioconductor submission.
detect_multiplets(): adaptive threshold detection of human-mouse multiplets from a 10x Cell Ranger GEM classification file, with diagnostic plots.
remove_multiplets_seurat(): annotate a Seurat object with the multiplet classification and optionally remove the detected multiplets.
Vignette illustrating the workflow on an example PDX dataset.