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RPy2 converter fromAnnData toSingleCellExperiment and back. (Fordetails about conversion see thedocs)

You can for example use it to process your data using bothScanpy andSeurat, as described in thisexample notebook

pip install anndata2ri# orconda install -c bioconda anndata2ri

If you have problems installing or importing anndata2ri,please make sure you first:

1. Check the stack trace:If the error happens while installing or importing a dependency such asrpy2,report your problem in that project’s bug tracker.
2. Search theissues.At the time of writing 17 of the 29 bugs (60%) are invalid or rpy2 bugs / install problems.
3. Make sure you have a compatible R version: rpy2 requires R ≥ 3.6.

Either use the converter manually …

importanndata2rifromrpy2.robjectsimportrfromrpy2.robjects.conversionimportlocalconverterwithlocalconverter(anndata2ri.converter):adata=r('as(some_data, "SingleCellExperiment")')

… or activate it globally:

importanndata2rifromrpy2.robjectsimportranndata2ri.activate()adata=r('as(some_data, "SingleCellExperiment")')

Activate the conversion before you load the extension:

importanndata2rianndata2ri.activate()%load_extrpy2.ipython

Now you can move objects from Python to R …

importscanpy.datasetsasscdadata_paul=scd.paul15()

%%R-iadata_pauladata_paul# class: SingleCellExperiment ...

… and back:

%%R-oadata_allendata(allen,package='scRNAseq')adata_allen<- as(allen,'SingleCellExperiment')

print(adata_allen)# AnnData object with ...