NEWS.md

In scFlex: Flexible Conversion Between Single-Cell Data Objects

scFlex 0.1.1

• Added automatic detection and joining of split Seurat v5 Assay5 layers such as counts.sample1, counts.sample2, and matching data.* layers.
• Counts-only Seurat objects can now be written to AnnData without normalization; counts are placed in X and layers["counts"] with an explicit conversion note.
• inspect_sc() now reports detected count and normalized-data layer groups for Assay5 objects.
• check_input_info() is retained as a compatibility wrapper but points users to inspect_sc().
• Improved assay-cell, feature-metadata, and reduction alignment during Seurat extraction.

scFlex 0.1.0

• Initial development release.
• Adds a common convert_sc() interface for Seurat, SingleCellExperiment, AnnData, and Loom.
• Preserves aligned counts, normalized expression, cell/feature metadata, and compatible dimensional reductions.
• Adds Seurat classic Assay <-> Assay5 conversion helpers.
• Uses reticulate::py_require() instead of a hard-coded Conda environment.

scFlex documentation built on Sept. 29, 2026, 5:10 p.m.