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whenever I run the batch removal method from a saved scGEN model, the output is always different from the trained model. any idea why this is the case?

TemiLeke

Errors while reading salmonella h5ad files

1

hello, while I am redoing the [scgen-reproducibility](https://github.com/theislab/scgen-reproducibility) notebooks **Fig 3**, I met some errors:    Could you help with this problem ？ Best

bitcometz

Hello, I am trying to run batch correction on some single-cell RNAseq data. This data has some cell type labels, so I thought the scGEN method would be a good...

johnjeang

Hi, I used MIX-Seq results data for drug perturbation of different cell lines to train the SCGEN model and select the indicated cell lines for prediction. After testing, the following...

GA-1101

When we choose a variety of cell types (e.g. batch_key is a cell type), whether SCGEN constructs a sub-model according to `batch_key`, or build a unified model based on all...

GA-1101

Questions on batch removal tutorial

2

Hi, I'm running the batch removal tutorial provided in: [https://scgen.readthedocs.io/en/latest/tutorials/scgen_batch_removal.html](url) My interest is the feature of you're software of producing a corrected expression matrix after the batch removal. I need...

Pazuzzilla

How to use data with categories unseen by a trained model

1

Hello, I am facing a problem with loading and passing data through a trained model when the data contains categories that were unseen by the model at training time. Specifically,...

majpark21

Hi scgen team, When I used the perturbation function, I found that the size of the predicted data is not consistent with the ground truth data, for example, the stim1...

XinyeZhao

TypeError: Can't instantiate abstract class SCGEN with abstract methods setup_anndata

1

I have been trying to merge multiple single cell data using scgen recently, but when I tried to run the tutorial, an error occurred，as follows, --------------------------------------------------------------------------- TypeError Traceback (most recent...

GGboy-Zzz

How to reproduce paper results

5

Hi，I am reproducing the results of your article, but I have encountered some environmental problems. As described in _https://github.com/theislab/scgen-reproducibility_, I recreated a virtual environment called _scgen-reproduce_ with packages tensorflow, scanpy,...

SZ-qing