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hubmapconsortium / tissue-bar-graphs

https://hubmapconsortium.github.io/tissue-bar-graphs/
MIT License
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Update HuBMAP Kidney data #4

Closed amberramesh closed 2 years ago

amberramesh commented 2 years ago

https://portal.hubmapconsortium.org/search?mapped_data_types[0]=snRNA-seq%20%5BSalmon%5D&mapped_data_types[1]=Slide-seq%20%5BSalmon%5D&origin_sample.mapped_organ[0]=Kidney%20%28Right%29&origin_sample.mapped_organ[1]=Kidney%20%28Left%29&entity_type[0]=Dataset (Requires access)

Additional datasets need to be run through Azimuth using: https://github.com/hubmapconsortium/hra-azimuth-predictions

Cell predictions file need to be run through an aggregator, such as https://github.com/hubmapconsortium/hra-azimuth-predictions

Add the aggregated counts for new datasets in the static branch https://github.com/hubmapconsortium/tissue-bar-graphs/tree/static/csv/Kidney_HuBMAP_Portal

vickydaiya commented 2 years ago

Some datasets do not have an h5 file on the server which results in a 404 error and terminates the program. Can I modify the download.py to skip over 404 errors and continue downloading other datasets by showing the "skipping dataset" message in the download log?

vickydaiya commented 2 years ago

Finished updating Kidney HuBMAP data on the portal HRA tissue blocks (05/18/22)