search

theislab / graphcompass

GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
MIT License
34 stars 0 forks source link

Cannot find the example data used in the MIBITOF_breast_cancer.ipynb #42

Closed huanlity closed 9 months ago

huanlity commented 9 months ago

Hi, very exciting work! I really want to test it out on our own data. First, I want to make sure I can reproduce the results in the tutorial notebook. However I could not locate the breast cancer .h5ad file from https://data.mendeley.com/datasets/d87vg86zd8/3. I downloaded the whole thing but still could not find the example data file. Please advise. Thank you so much and good luck with the paper review!

Huan Wang Broad Institute

merelkuijs commented 9 months ago

Hi Huan, thanks for reaching out! We built the .h5ad file from the .csv file present in that repo. We can probably upload the processing notebook here. I'll let you know when that's online.

merelkuijs commented 9 months ago

Hi Huan, please find the processing notebook in the notebooks/processing folder. There we show how to build the adata from the raw files you can download from the Mendeley repo. I hope that helps.

Let me know if you have any further questions.

huanlity commented 9 months ago

Thanks a lot!

Huan

On Thu, Feb 15, 2024 at 6:05 PM Merel Kuijs @.***> wrote:

Hi Huan, please find the processing notebook in the notebooks/processing folder. There we show how to build the adata from the raw files you can download from the Mendeley repo. I hope that helps.

Let me know if you have any further questions.

— Reply to this email directly, view it on GitHub https://github.com/theislab/graphcompass/issues/42#issuecomment-1947483244, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJBB25GNKGTFO57SIXOPO3YT2IE5AVCNFSM6AAAAABDFDTFH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBXGQ4DGMRUGQ . You are receiving this because you authored the thread.Message ID: @.***>