Closed davemcg closed 4 years ago
@davemcg I had the same error after following the install instructions. This line is the only place I saw the version of anndata matter for sceasy
I just upgraded to the newest anndata (anndata==0.7.1
) and the function sceasy::convertFormat(seurat_object, from="seurat", to="anndata", outFile='filename.h5ad')
which appears to work just fine.
@davemcg Dependency requirement in bioconda for anndata < 0.6.20 is largely for full conversion (carrying over almost all slots, including those in .uns
) between anndata and loom. For other conversions, anndata >= 0.6.20 is fine. We haven't tested with anndata>=0.7, but good to know it works for your data @nathanin. We probably can relax the requirement for anndata in the next release.
There's an issue with the anndata install.
I'm installing with: conda create --yes --name sceasy; conda activate sceasy; conda install -c bioconda r-sceasy==0.0.5
When I enter python and
import anndata
I get this error:ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils'
This appears to be an scipy/anndata issue that was later resolved, but we have to use
anndata 0.6.19
withsceasy
. What should I do to ameliorate this?