datasets failed to download

[UnkownNames]

Good job,when I run the tutorial the url http://zhanglab.net/scalex-tutorial/pbmc.h5ad ,http://zhanglab.net/scalex-tutorial/pancreas.h5ad and http://zhanglab.net/scalex-tutorial/pancreas_query.h5ad is unavailable, for example ,it returns

[jsxlei]

Apologies for the inconvenience with the data download. Please find below the alternative links to download the files. https://www.dropbox.com/scl/fi/dnwpv29kcfl449a8aikqi/pancreas.h5ad?rlkey=9me8xa0n1f3lz8qqornkh0ae0&dl=0 https://www.dropbox.com/scl/fi/obdt0ecjjlis6tyekyzyy/pancreas_query.h5ad?rlkey=cwik9m5kqrookmi84vdmwhnqk&dl=0

Let me know if you have any questions.

[aminbensaad]

Hi @jsxlei , You did some great work here! I am considering including it in my work on scATAC batch effects at Theislab in Munich's Helmholtz Center.

Unfortunately, the Mouse Brain dataset cannot be downloaded from the 'Integrating scATAC-seq data using SCALEX part of the tutorial.(see image)

I am a bit in a hurry as my stay is going to end soon. So I'd be extremely grateful if you could provide it in the next days. 🙏

[jsxlei]

Hi, thank you for your interest in SCALEX. The original link is broken. You can use this link to download the data you need https://www.dropbox.com/scl/fi/affgmiktg49s3ogmzq8ss/mouse_brain_atac.h5ad?rlkey=iejewl06wuvnflyqfj2rgabwi&dl=0.

[aminbensaad]

Thank you so much! :)

[aminbensaad]

Hey @jsxlei, do you also have the processed result of the Integration cross-modality data using SCALEX[] ?

I'd need the adata object with peak information on chr, start and end too as I am benchmarking with models that need this information.

[jsxlei]

You can follow this tutorial https://scalex.readthedocs.io/en/latest/tutorial/Integration_cross-modality.html to get the processed data you want.