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10.1038/s41591-019-0750-6 #514

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LisaSikkema opened this issue Feb 4, 2022 · 5 comments · May be fixed by #599
Open

10.1038/s41591-019-0750-6 #514

LisaSikkema opened this issue Feb 4, 2022 · 5 comments · May be fixed by #599
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@Lihua1990
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dataset workshop

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@LisaSikkema
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Laughney et al.
Regenerative lineages and immune-mediated pruning in lung cancer metastasis
https://www.nature.com/articles/s41591-019-0750-6

Data:
https://s3.amazonaws.com/dp-lab-data-public/lung-development-cancer-progression/PATIENT_LUNG_ADENOCARCINOMA_ANNOTATED.h5)https://s3.amazonaws.com/dp-lab-data-public/lung-development-cancer-progression/PATIENT_LUNG_ADENOCARCINOMA_ANNOTATED.h5
@Lihua1990
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I will try this, thanks!

@Lihua1990
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The data links should be:

https://s3.amazonaws.com/dp-lab-data-public/lung-development-cancer-progression/PATIENT_LUNG_ADENOCARCINOMA_ANNOTATED.h5

https://s3.amazonaws.com/dp-lab-data-public/lung-development-cancer-progression/MOUSE_LUNG_ADENOCARCINOMA_METASTASIS_ANNOTATED.h5

The authors also provide GEO accession number GSE123904

I suppose I can use the two links above and ignore the GEO accession number?

@davidsebfischer
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We do actually believe that GEO is preferable as a data source to this s3 link as GEO is very constant. So if there is equivalent raw data on GEO, I would choose GEO as a source.

@Lihua1990
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I am using this https://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123904/suppl/GSE123904_RAW.tar for downloading the data

@Lihua1990
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Though not finished, I have sent a pull request: #599

Hope it will be a bit help!

@le-ander le-ander linked a pull request Feb 16, 2022 that will close this issue
10_1038_s41591_019_0750_6 #599
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10_1038_s41591_019_0750_6 dlhlisa/sfaira
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@davidsebfischer @le-ander @Lihua1990 @LisaSikkema