What's going on with the widespread use of the log(X + 1) transform for NGS data?

• gemelli

  2 64 7.0 Python

  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.

  

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.

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

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