search

theislab / sfaira

data and model repository for single-cell data
https://sfaira.readthedocs.io
BSD 3-Clause "New" or "Revised" License
134 stars 11 forks source link

10.1038/s41591-019-0750-6 #514

Open LisaSikkema opened 2 years ago

LisaSikkema commented 2 years ago

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 commented 2 years ago

I will try this, thanks!

Lihua1990 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

Lihua1990 commented 2 years ago

Though not finished, I have sent a pull request: https://github.com/theislab/sfaira/pull/599

Hope it will be a bit help!