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linnarsson-lab / adult-human-brain

Cytograph version used for adult human-brain analysis
BSD 2-Clause "Simplified" License
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Extract clusters from aggregated loom #6

Closed mperalc closed 1 year ago

mperalc commented 1 year ago

Thanks very much for this resource, it is very useful. I'm not very familiar with the loom format and after looking at the aggregate loom object (genes x clusters) I can't seem to find the cluster names. Could you let me know how to extract this information? Thanks again.

rmd13 commented 1 year ago

This is stored in a excel file inside this repo. cluster_annotation.xlsx. You need to add this table into the loom file as scalar data (float or string of variable length) by your favirote hdf5 programming languages. I have done this today.

To insert the information from cluster_annotation.xlsx into genes x cells is more complicated. For each cell, the corresponding cluster information in excel file needs to be packed line-after-line. This will finally get a huge table with millions of duplication. Then each column could be injected into the very large raw loom file as a separated scalar table (float or string of variable length) . Then the loom file could be used for analysis in other platforms. I have also done this today. The coding takes my time from noon to midnight,

mperalc commented 1 year ago

Thanks!