Add environment for anndata v0.10.9. This is now the default environment for the Python reader/writer.
Avoid deprecation warning due to setting dtype when creating Python
AnnData objects
Standardise code styling using styler
Add test using the more complete example H5AD file
Correctly assign levels to factors in R reader with anndata v0.7 files
Correctly set filepath in the R reader with reading
adata.raw' with use_hdf5 = TRUE (PR from @GabrielHoffman)
Add environment for anndata v0.10.6. This is now the default environment for the Python reader/writer.
Improve warnings when converting matrices fails
Minor change to writing DelayedArray matrices for compatibility
with HDF5Array >= v1.31.1
Correctly handle use_backed = TRUE with newer anndata
versions
Correctly instantiate the anndata v0.10.2 environment
Minor fixes for typos etc.
Add environments for anndata v0.9.2 and v0.10.2. Version 0.10.20 is now the default envrionment for the Python reader/writer.
Changes for compatibility with rhdf5 v2.45.1 including enum types that simplifies reading of nullable types in the native R reader
Dimensions are now passed correctly when converting the raw slot
Backed sparse matrices are now converted in AnnData2SCE()
Add compatibility with the anndata v0.8 H5AD format to the the native R writer (By @jackkamm and @mtmorgan)
Add functions for converting pandas arrays used by anndata when arrays have missing values
Add Robrecht Cannoodt and Jack Kamm as contributors!
Minor adjustments to tests to match reader changes
Improve compatibility with the R anndata package. This required modifying conversion functions so that Python objects are explicitly converted rather than relying on automatic conversion.
Added support for numpy recarrays. This solves a long-standing
issue and allows results from scanpy's rank_genes_groups()
function to be read.
The Python version is now pinned in the anndata v0.7.6 environment for compatibility with changes in basilisk
Instatiate Python environments so they can be properly picked up by
basilisk::configureBasiliskEnv()
Allow missing obs/var names when use_hdf5 = TRUE
Minor changes to the UI functions for compatibility with cli v3.4.0
Minor changes for compatibility with Matrix v1.4-2
Improvements to the UI for warnings
Updates and improvments to tests
Added support for multiple basilisk environments with different
anndata versions. Users can now specify the environment to use with
options in readH5AD() and writeH5AD(). To faciliate this
some exported objects where converted to functions but this should only
effect developers.
Updated the default environment to use anndata v0.8.0. This is a major update and files written with v0.8.0 cannot be read by previous anndata versions. This was the motivation for supporting multiple environments and users can select the previous environment with anndata v0.7.6 if compatibility is required.
Standardise naming in AnnData2SCE(). Column names of data frames
and names of list items will now be modified to match R conventions
(according to make.names()). When this happens a warning will be
issued listing the modifications. This makes sure than everything in the
created SingleCellExperiment is accessible.
Allow data.frame's stored in varm to be converted in
SCE2AnnData()
Minor updates to the vignette and other documentation.
Updates to tests to match the changes above.
Add arguments to control how slots are converted in AnnData2SCE()
and SCE2AnnData(). Each slot can now be fully converted, skipped
entirely or only selected items converted.
Add support for converting the raw slot to an altExp in
AnnData2SCE()
Add recursive conversion of lists in AnnData2SCE()
Add progress messages to various functions. These can be controlled by function arguments or a global variable.
Add long tests for various public datasets. This should help to make the package more robust
Fix bug in converting dgRMatrix sparse matrices
Correctly handle DataFrame objects stored in adata.obsm
Update anndata and other Python dependencies, now using anndata v0.7.6
Improved conversion checks for all slots in AnnData2SCE()
Enable return conversion of the varm slot in AnnData2SCE()
Avoid converting obsp and varp to dense matrices in
AnnData2SCE()
AnnData2SCE() should now always return dgCMatrix matrices
when assays are sparse
More consistent conversion of metadata to uns in
SCE2AnnData()
Handle conversion of list columns in colData and rowData in
SCE2AnnData()
Better support for converting anndata SparseDataset arrays
Improved support for conversion of HDF5 backed AnnData objects
Better support for writing DelayedArray assays in
writeH5AD()
Store X_name in AnnData2SCE() for use by
SCE2AnnData() and add an X_name argument to
AnnData2SCE() and readH5AD()
Add a compression argument to writeH5AD()
Add an experimental native R reader to readH5AD()
Export zellkonverterAnnDataEnv for use by other packages
Accepted into Bioconductor for Release 3.12
zellkonverter provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.