scgen issues

scgen Literal deprecation error

1

In the latest version it of scgen (2.1.0) it shows the following error when trying to import the module. DeprecationWarning Traceback (most recent call last) Cell In [1], line 2...

abuchin

difference between SCGEN and SCGENVAE

Hello! Thanks for your nice tool! Could you please tell me the difference between scgen.SCGEN and scgen.SCGENVAE? I am now following the tutorial to train a model for perturbation prediction...

huawen-poppy

Question about get_decoded_expression() and predict() functions

Hi, Could you pls explain the difference between the two functions: get_decoded_expression() and predict()? It appears to me that both functions take control gene expressions as input and produce post-perturbation...

znavidi

Error in network.batch_removal() due to missing positional argument in AnnData.concatenate()

5

Hello, I'm encountering an issue while using scgen for batch correction. The training part works fine, but I'm facing an error when calling network.batch_removal(). The error message is as follows:...

macelik

change python-igraph to igraph

Please see https://github.com/igraph/python-igraph/issues/699 for an explanation.

szhorvat

Update depreciated `AnnData.concatenate`

2

Hello, The depreciated method `AnnData.concatenate` is used when running `batch_removal` (see [here](https://github.com/theislab/scgen/blob/master/scgen/_scgen.py#L268)). This only throws a warning with `anndata==0.9` and `pandas

quentinblampey