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biosurf / cyCombine

Robust Integration of Single-Cell Cytometry Datasets
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Question about the example datasets #57

Open paodan opened 1 month ago

paodan commented 1 month ago

Dear authors,

Thanks for developing such a great package for dealing with the batch effects and multi-panel integration. While studying the vignette, I have difficulties to make my data similar to the data that you used in the vignette. Would it be possible to share the raw data (.fcs, panel, metadata, etc) so that I can fully follow the vignette? Thank you in advance!

cbligaard commented 1 month ago

Hi,

Thanks for the kind words. All the cytometry data (FCS) in the manuscript should be publicly available as listed here: https://www.nature.com/articles/s41467-022-29383-5#data-availability. If you're referring to metadata and panels, the file format is described here: https://biosurf.org/cyCombine_ref_manual.html with an example of the panel data here: https://biosurf.org/cyCombine_CyTOF_1panel.html. The metadata for the DFCI data is also uploaded in FlowRepository.

I hope it helps - but let us know if you need assistance in loading your own data.

paodan commented 1 month ago

Thank you. I will have a look into them.