Request code for Simulated Data and data Preprocessing

[Rumi07]

Dear Author,

Thank you for your excellent work. I'm truly interested in exploring your work further.

I was wondering if you would kindly share the code used to generate the simulated SRT data, particularly the six distinct spatial patterns described in the paper. Access to this simulation code would be immensely helpful for better understanding and reproducing your experiments.

Additionally, if possible, I would greatly appreciate it if you could share any data preprocessing code or scripts you used in your pipeline.

Thank you for your time and consideration. Any kind of help would be sincerely appreciated.

[Devin-jun]

Sorry for the late reply. Thank you for your interest in our work. We have uploaded the simulated data to the figshare. you can download it from the following link: DUSTED Simulated Data.

For data preprocessing, we followed these key steps using the Scanpy package:

sc.pp.highly_variable_genes(adata, n_top_genes=2000,
flavor="seurat_v3")
sc.pp.normalize_total(adata, ,target_sum=1e4)
sc.pp.log1p(adata)

We hope these resources will be helpful for your research.

[Rumi07]

@Devin-jun , Thank you for your response. It was very helpful.

• I would be sincerely grateful if you could kindly share the code used to simulate the synthetic datasets using SymSim and scCube.

• Additionally, could you please provide the download link for the HOCWTA dataset? I would also appreciate any brief instructions on how and which specific files were used in your work.

Any assistance you can provide would be greatly appreciated.