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theislab / sfaira

data and model repository for single-cell data
https://sfaira.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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10.1186/s13059-020-02006-2 #504

Open Hrovatin opened 2 years ago

Hrovatin commented 2 years ago

Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets https://doi.org/10.1186/s13059-020-02006-2 Data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142465 Known mistakes in cell type annotation on GEO Re-aligned counts: mouse: /storage/groups/ml01/projects/2020_pancreas_karin.hrovatin/data/pancreas/scRNA/GSE142465/scanpy_AnnData/SRR107515/ human: /storage/groups/ml01/projects/2020_pancreas_karin.hrovatin/data/pancreas/scRNA/GSE142465_human/scanpy_AnnData/SRR10751/ mouse, human pancreatic islet healthy, chemical stress

roubido commented 2 years ago

i read this message on slack "We just realized that you cannot assign yourself to an issue if you are not member of our GitHub organisation, just comment on the issue and then we will assign you! "

so I am leaving my comment to this dataset.

le-ander commented 2 years ago

Hey, the workshop just finished but feel free to have a go at writing a dataloader for this dataset! Everything you need to know should be here: https://sfaira.readthedocs.io/en/latest/adding_datasets.html#