isoplex 0.1.0

Compute and filter isoforms or other features based on perplexity

Isoform Perplexity

Compute and filter isoforms based on perplexity

• Free software: MIT License
• Documentation: https://fairliereese.github.io/isoplex/

Features

This library implements the basic computations described by Schertzer et al. in their manuscript. In brief, from a counts or TPM expression matrix of transcriptome features (transcript isoforms, ORF ids, protein IDs, etc) and their associated genes, isoplex will compute the gene potential, entropy, perplexity, and mark effective features based on the aforementioned metrics.

These metrics are designed to provide a more intuitive description of isoform diversity as well as to provide a less rigid framework for filtering isoforms, as the distribution of expression values are taken into account for each gene to mark isoforms as effective or not, rather than applying a uniform filter across the entire dataset.

Credits

This package was created with Cookiecutter and the audreyfeldroy/cookiecutter-pypackage project template.