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Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
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Release 3 16 #58

Closed yduanBioinfo closed 8 months ago

yduanBioinfo commented 10 months ago

Add support for h5seurat format to TENxMatrix object. In this version, only functions in TENxMatrix-class and TENxMatrixSeed-class has been changed. At the same time, I have added a toy data and written some example codes in the help document.

As a concern, the change in .find_rownames_dataset of TENxMatrixSeed-class is a little dangerous. I'm afraid that the 'features' prior than 'features/id' will cause a bug. However, if set 'feature/id' prior, it will cause an error: "Error in H5Lexists(fid, name) : HDF5. Links. Can't get value". If the bug actually exist, it's maybe a solution to write a new function .read_h5seurat_component to read h5seurat data separately as in my last pull request.

hpages commented 9 months ago

Thanks @yduanBioinfo, and sorry for the delay.

Why is the PR against the RELEASE_3_16 branch? BioC 3.16 was frozen about 6 months ago and is no longer supported. Do you think you can make a PR against the devel branch instead? Also please use a meaningful title for the PR.

Thanks again, H.

yduanBioinfo commented 8 months ago

I have made a new PR against the devel branck.