leihouyeung/sd2

sd2's Issues

Simulated dataset

Hello dear author!
You describe the generation of the simulated data set in detail in your paper, can you advise what tools are used to generate this simulated data

Dependence of SD2

Hi,

Thanks for your novel wrok, and Could you please share the SD2's dependence?

Best

Can you provide the data used in the experiment?

If you can provide processed data that can be used directly by the model, you will be greatly appreciated.

The problem about the data 'PDAC_GSM4100721.rds'

Hi,
It's a very good method to do transcriptomics deconvolution ! Now, I can not find the data ‘PDAC_GSM4100721.rds’，can you share it with me ? Thank you very much !

Missing environment reqruirements

Hi,
I could not find requirements file with dependencies and their versions. Could you please push them? I am unable to run the code with my tensorflow version (2.4.1).
Thanks!

Issues while running the code

Dear authors,

We are running SD for spot deconvolution task. However, we are running into few errors.

1. There is an error in line 491 in gutils.py: “Linked_graph2.csv” is missing. We have searched all the files in the GitHub, we could not find where this file is getting generated. However, we did find for Linked_graph1.csv and not for Linked_graph2.csv. Could you please help us resolve this issue?
2. We would also like to highlight that class name is mentioned as “DSTG” in import statement in train.py. We corrected it to SD2. We have also added gutils in import and tf.compat.v1 which is needed for successful run.

Thanks,
Ajita