Is it possible to use the data without a biom as input

biocore / gemelli

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

BSD 3-Clause "New" or "Revised" License

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Is it possible to use the data without a biom as input #74

Open SilasK opened 10 months ago

SilasK commented 10 months ago

For the python input it would be great if a simple pandas table or numpy array could be used as input.

cameronmartino commented 10 months ago

Hi @SilasK,

The issue is loading in large sparse tables. We chose biom as a requirement because these tools were developed for microbiome data and loading mostly zeros into memory is a pain. However, I can see the ease of use in the next version or the one after we will consider allow both types as input. At least for the Python API, since the data is already loaded.

harper357 commented 8 months ago

In case you didn't know, Pandas does have a sparse format.