rglab/covid19_sc

Processing workflow for COVID-19 single cell data

covid19_sc's Issues

I need the Merged dataset, but the download link is broken.

We will be periodically adding relevant COVID-19 single-cell datasets to the web portal. If you know of a publicly-accessible dataset that you would like to see included, you may request it here. If you have any additional information that you would like to share, you may contact us at [email protected].

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Unable to read the merged dataset through R

Hi,

I downloaded the merged dataset (covid19_datasets.tar.gz) from the website (https://atlas.fredhutch.org/fredhutch/covid/), but I'm unable to read the datafile into SingleCellExperiment through R. I used

Read10X_h5(filename="covid19_datasets.tar.gz")

but it returns

Error in `[[.H5File`(infile, paste0(genome, "/data")) : 
  An object with name active.ident/data does not exist in this group

I was also unable to read all the hdf5 files on the website too with Read10X_h5, it gave me the same error. May I know how to fix it? My Seurat version is 4.1.1, and my R version is 4.2.0.