anndataR 0.2.0
Breaking changes
- Switch the HDF5 back end to use the {rhdf5} package instead of {hdf5r} (PR #283, Fixes #272, #175, #299)
- This addresses various issues related to H5AD files and allows better integration with Bioconductor. Most of the previous known issues have now been resolved.
- It also greatly improves compatibility with H5AD files written by Python anndata
- NOTE: Make sure to install {rhdf5} instead of {hdf5r} to be able to read and write H5AD files!
Major changes
- Updates for compatibility with Python anndata >= 0.12.0 (PR #305, Fixes #304)
- Add helpers for reading/writing
NULL
values to/from H5AD files - Writing of
NULL
values can be disabled by settingoption(anndataR.write_null = FALSE)
to allow the files to be read by Python anndata < 0.12.0
- Add helpers for reading/writing
- A
counts
ordata
layer is no longer required duringSeurat
conversion (PR #284)- There will still be a warning if neither of this is present as it may affect compatibility with {Seurat} functions
anndataR 0.1.0 (inital release candidate)
Initial release candidate of {anndataR} including:
- Native reading and writing of H5AD files
- R implementations of
InMemoryAnnData
andHDF5AnnData
objects - Conversion between
AnnData
andSingleCellExperiment
orSeurat
objects - Extensive function documentation and vignettes demonstrating usage
- Comprehensive unit testing and identification of known issues