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theislab / mubind

Learning motif contributions to cell transitions using sequence features and graphs.
https://mubind.readthedocs.io
MIT License
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Improve documentation of pancreas multiome dataset #133

Open MUCDK opened 3 weeks ago

MUCDK commented 3 weeks ago

Please document the datasets better, especially the pancreas multiome, as it's not officially published yet (will be end of the year together with the moscot paper). So please explicitly refer to the moscot preprint in the docs. The raw data is now available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE275562

ilibarra commented 3 weeks ago

@MUCDK Thanks for the suggestion! The ref. for each dataset is now at the beginning of each training notebook using the {cite} syntax e.g. https://mubind.readthedocs.io/en/latest/notebooks/single_cell/02_2_1_scatac_multiome_pancreas_priors_train.html https://mubind.readthedocs.io/en/latest/references.html Thank you for the GEO link. We also included it in the panc. endocrinogenesis tutorial as well. Indicate if you mean additional documentation for the datasets and/or examples from other repos. We'll keep improving docs based on that.