Download

Here are download links for software and data resources we were involved in developing.

Software

  • BBERT – Fast and accurate taxonomic domain assignment of short metagenomic reads, also inferring whether the read is coding or not and for coding reads, their reading frame.
  • CompoRes – an algorithmic package designed to analyze the connection between changes in the host’s microbiota and the host’s gene expression. It addresses two significant analysis challenges: compositional statistics in the microbiota, and multiple hypothesis testing which results in false correlations between microbiota and host.
  • CorrEnrich – (Correlation Enrichment) is a Python toolkit for identifying and evaluating biologically meaningful gene clusters by analyzing their expression tightness, functional enrichment (via GO terms), and statistical significance under various experimental conditions.
  • Companion Jupyter python notebooks demonstrating key model simulations, bundled with the manuscript “Mathematical modeling and intuition in microbiology: a perspective”.
  • Code and data for the manuscript “Grow now, pay later: when should a bacterium go into debt?“. Also in Zenodo.

Data