Python rclr Projects

gemelli

2 65 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.

Project mention: What's going on with the widespread use of the log(X + 1) transform for NGS data? | /r/bioinformatics | 2023-05-22

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.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).