More detailed Norman 2019 preprocessing notebook#3
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yugeji merged 3 commits intotheislab:mainfrom Mar 31, 2022
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March 25, 2022 14:39
This PR adds a notebook to download + preprocess the Norman 2019 dataset starting directly from downloading the raw counts. The notebook currently downloads the data, and fills in various metadata values. I made this PR as the current Norman 2019 notebook depends on downloading another h5ad file first- I personally like being able to see the full workflow (i.e., going from author provided files to final anndata) as part of the notebooks. As mentioned in theislab#2, I'm not sure what QC steps you prefer so this notebook simply produces an anndata with raw counts.
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ethanweinberger
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ethanweinberger
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Wow, thank you so much! I really appreciate how well-commented and legible your notebook is, and you were really thorough with aligning the dataset with the paper! |
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This PR adds a notebook to download + preprocess the Norman 2019
dataset starting directly from downloading the raw counts. The
notebook currently downloads the data, and fills in various metadata
values. I made this PR as the current Norman 2019 notebook depends
on downloading an h5ad file with (already filled in) metadata, and I think it's more instructive
for people to be able to see the full workflow (i.e., going from author provided
files to final anndata) as part of the notebooks. Happy to combine this with
the original Norman notebook before merging of course- for now I made a new one while
waiting for answers to the questions in #2.