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gemelli reviews and mentions
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What's going on with the widespread use of the log(X + 1) transform for NGS data?
You might want to look into the robust CLR in gemelli and the associated papers. Basically, it only does the CLR on the cells with values, then does sparse matrix completion ML (a la recommendation engines) to fill in the nulls. The devil is in the details of the ML algorithm, but at least it’s not deep learning. I do get pretty nice plots and correlations from the output distance matrices, so there is that.
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Understanding why CLR followed by correlation is not compositionally-valid
You might want to look into Gemelli for something that tries to thread that needle.
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biocore/gemelli is an open source project licensed under BSD 3-clause "New" or "Revised" License which is an OSI approved license.
The primary programming language of gemelli is Python.
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