Question

reading hdf5 files without hdf5r

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Bogdan ▴ 670

@bogdan-2367

Last seen 13 months ago

Palo Alto, CA, USA

Dear all,

is there a way to read the hd5 files in R without using hdf5r library ?

Thanks,

Bogdan

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hdf5r • 2.7k views

ADD COMMENT • link updated 2.6 years ago by Hervé Pagès 16k • written 2.6 years ago by Bogdan ▴ 670

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Why? What's the problem with hdf5r?

ADD REPLY • link 2.6 years ago Gordon Smyth 51k

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Hi Gordon,

If BioC mailing list does not mind, I have just described the problem that I do encounter on stackoverflow :

https://stackoverflow.com/questions/72074106/hdf5r-libhdf5-hl-so-200-cannot-open-shared-object-file

Any suggestions please ?

ADD REPLY • link 2.6 years ago Bogdan ▴ 670

score 2 · Answer 1 · 2022-05-01

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Gordon Smyth 51k

@gordon-smyth

Last seen 7 hours ago

WEHI, Melbourne, Australia

I use the Bioconductor package rhdf5 instead the CRAN package hdf5r.

ADD COMMENT • link 2.6 years ago Gordon Smyth 51k

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Hi Gordon,

thank you for your suggestions. I would love to use rhdf5 instead of hdf5r, although packages such as Seurat or Signac requiire hdf5r, for example :

> library("Signac")
> counts <- Read10X_h5(filename = "file.h5") 

Error in Read10X_h5(filename = "/home/btanasa/) :
  Please install hdf5r to read HDF5 files

ADD REPLY • link 2.6 years ago Bogdan ▴ 670

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So it sounds like you actually want to use CRAN package hdf5r but your original question suggests that you are looking for an alternative to hdf5r. Kind of confusing!

ADD REPLY • link 2.6 years ago Hervé Pagès 16k