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Changelog

Source: NEWS.md

scConvert 0.1.0

Release Date: 2026-03-10

Highlights

Initial public release of scConvert — a universal single-cell format converter for R.

Universal Format Conversion

  • Support for 7 formats: h5ad, h5Seurat, h5mu, Loom, Zarr, RDS, and SingleCellExperiment
  • Hub architecture with 30+ conversion paths via scConvert()
  • Direct HDF5 paths for h5ad/h5Seurat without intermediate loading

Direct h5ad Loading

  • readH5AD() for native h5ad-to-Seurat conversion without intermediate files
  • Sparse (CSR/CSC) and dense matrix support
  • Categorical metadata, dimensional reductions, neighbor graphs, and spatial data

MuData (h5mu) Multimodal Support

  • readH5MU() / writeH5MU() for multimodal single-cell data
  • Automatic modality-to-assay name mapping (rna->RNA, prot->ADT, atac->ATAC)
  • No MuDataSeurat or Python dependency required

Zarr AnnData Support

  • readZarr() and writeZarr() for Zarr-based AnnData stores (v2 format)
  • Sparse CSR/CSC and dense matrix support
  • Categorical metadata and dimensional reduction preservation

Spatial Data (Visium)

  • Bidirectional Visium spatial data conversion with image reconstruction
  • Proper coordinate handling and scale factor preservation
  • Compatible with scanpy/squidpy spatial analysis workflows

C CLI Binary

  • Standalone scconvert binary for h5ad/h5Seurat/h5mu conversions
  • Streaming on-disk conversion without R or Python runtime
  • Options: --assay, --gzip, --overwrite, --quiet

BPCells On-Disk Loading

  • readH5AD(..., use.bpcells = TRUE) for memory-efficient atlas-scale analysis
  • Compatible with all Seurat analysis functions

Seurat v5 Compatibility

  • Full support for Seurat v5 Assay5 objects
  • Proper handling of V5 layered data structure in conversions