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2 hours ago by

I am trying to import single-cell data from the human cell atlas (e.g, www.covid19cellatlas.org/#vento18-10x).

I want to use this files within Seurat, however - I keep getting this error:

> kidney <- ReadH5AD("documents/Datasets/Kidney/")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: ../../src/hdf5-1.10.0-1/src/H5F.c in H5Fopen(): line 579: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: ../../src/hdf5-1.10.0-1/src/H5Fint.c in H5F_open(): line 1208: unable to read superblock
        class: HDF5
        major: File accessibilty
        minor: Read failed

    error #002: ../../src/hdf5-1.10.0-1/src/H5Fsuper.c in H5F__super_read(): line 271: unable to locate file signature
        class: HDF5
        major: File accessibilty
        minor: Not an HDF5 file

    error #003: ../../src/hdf5-1.10.0-1/src/H5FDint.c in H5FD_locate_signature(): line 124: unable to read file signature
        class: HDF5
        major: Low-level I/O
        minor: Unable to initialize object

    error #004: ../../src/hdf5-1.10.0-1/src/H5FDint.c in H5FD_read(): line 217: driver read request failed
        class: HDF5
        major: Virtual File Layer
        minor: Read fai

Any ideas how to read in H5AD files? This has been pretty challenging for me to figure out.

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modified 2 hours ago

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