Conversion between scRNA-seq objects
DelayedArray
matrices for compatibility with {HDF5Array} >= v1.31.1use_backed = TRUE
with newer anndata versions (Fixes #114)Full Changelog: https://github.com/theislab/zellkonverter/compare/v1.12.0...v1.14.0
raw
slot (Fixes #96)AnnData2SCE()
(Fixes #96)Full Changelog: https://github.com/theislab/zellkonverter/compare/v1.10.0...v1.12.0
Full Changelog: https://github.com/theislab/zellkonverter/compare/v1.8.0...v1.10.0
rank_genes_groups()
function to be read. (PR #81, fixes #45, #28)basilisk::configureBasiliskEnv()
(Fixes #66)obs
/var
names when use_hdf5 = TRUE
(Fixes #65)Full Changelog: https://github.com/theislab/zellkonverter/compare/v1.7.0...v1.8.0
readH5AD()
and writeH5AD()
. To faciliate this some exported objects were converted to functions but this should only affect developers.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 SingleCellExperiment
is accessible.data.frame
's stored in varm
to be converted in SCE2AnnData()
Full Changelog: https://github.com/theislab/zellkonverter/compare/v1.4.0...v1.6.0
AnnData2SCE()
and SCE2AnnData()
. Each slot can now be fully converted, skipped entirely or only selected items converted. (#47)raw
slot to an altExp
in AnnData2SCE()
(#53, #57)AnnData2SCE()
dgRMatrix
sparse matrices (#55)DataFrame
objects stored in adata.obsm
Full Changelog: https://github.com/theislab/zellkonverter/compare/v1.2.0...v1.4.0
AnnData2SCE()
(See #45)varm
slot in AnnData2SCE()
(Fixes #43)obsp
and varp
to dense matrices in AnnData2SCE()
AnnData2SCE()
should now always return dgCMatrix
matrices when assays are sparse (Fixes #34)metadata
to uns
in SCE2AnnData()
(Fixes #40)colData
and rowData
in SCE2AnnData()
(Fixes #26)SparseDataset
arrays (PR #41, Fixes #37, Fixes #42)AnnData
objectsDelayedArray
assays in writeH5AD()
(PR #35, Fixes #32)X_name
in AnnData2SCE()
for use by SCE2AnnData()
and add an X_name
argument to AnnData2SCE()
and readH5AD()
(Fixes #7)compression
argument to writeH5AD()
(Fixes #49)readH5AD()
zellkonverterAnnDataEnv
for use by other packages (Fixes #38)First Bioconductor release of {zellkonverter}
{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.