Finish table of chem and align

epaaso / sc-luca-explore

Exploring the luca dataset for building coabundance networks

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Closed epaaso closed 3 months ago

epaaso commented 1 year ago

[x] Must read all methods of the papers to get the chem and alignment
[x] Also it is important to see why we lose so many genes when getting from biomart (The docs use the annotation that comes with the atlas so that is better)
[x] Get the stage and whether it is squamous or adeno

epaaso commented 1 year ago

Some datasets don't have the info of stage or type of cancer. Chen2020 does not have one and they didn't respond to an email requesting their data

epaaso commented 8 months ago

We can use the Integrated dataset and do some .groupby of the .obs dataframe to extract all we need. The do have the info for Chen also.

epaaso commented 3 months ago

Finished in cf5e7838e66822f02c0f1b0d9f1a926db5b9c6bb