Functions to aid in converting Seurat objects to AnnData objects
milescsmith / s2a Goto Github PK
View Code? Open in Web Editor NEWSeurat to AnnData conversion
License: Other
Seurat to AnnData conversion
License: Other
Greetings,
Thanks for putting this together.
I followed the installation from https://rdrr.io/github/milescsmith/s2a/:
install.packages("remotes")
remotes::install_github("milescsmith/s2a")
However, when I try to load the library, I get an error:
> library(s2a)
Error: package or namespace load failed for ‘s2a’:
.onLoad failed in loadNamespace() for 's2a', details:
call: py_module_import(module, convert = convert)
error: ModuleNotFoundError: No module named 's2a'
>
Is there a python module to also install?
Thanks!
JP
Hi, primary AnnData author and anndata2ri author here. Cool project!
Is there any comparison of the features of SeuratObject, SingleCellExperiment and AnnData? We should work together to not lose anything the respective other has.
Also check out theislab/anndata2ri#8. I spent way too much time compiling this information to not share it
it's an impressive package to convert structure from Seurat to Anndata. But recently, when I used convert_to_anndata
implmented in s2a
. I got errors as following:
Error in py_call_impl(callable, dots$args, dots$keywords) :
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
Detailed traceback:
File "/home/user/.local/lib/python3.6/site-packages/s2a/convert.py", line 76, in add_reduction
if feature_loadings and feature_loadings.size > 0:
Can you help me work it out?
Thanks a lot
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