prettyClusters

A tool for categorizing and exploring genomic neighborhoods in a sequence-independent way. Includes additional modules for provisional identification of hypothetical protein families, data input from GenBank and IMG formats, and generation of vector figures for genomic neighborhood visualization. Fills a few niches - inclusion of information about hypothetical proteins, lack of reliance on known gene cluster structure, sequence independence - that don't quite come together in other tools. Set up as an R package, publicly available on GitHub. Questions, feedback and contributions are very welcome - it's under active development!

magSearch and magQuant

Simple pipeline for identifying representatives of an enzyme family in metagenomic and metatranscriptomic datasets, quantifying them, and preparing hits on large enough contigs for exploration via prettyClusters. Derived from approaches developed in the Balskus group. Currently a (private) set of cluster-specific shell scripts on GitHub; updates expected winter 2023-2024.

instrumentUtilities

A set of R scripts for automatic processing of exported files for FPLC, LC, LC-MS, and UV-vis chromatograms and spectra from some common vendors. Currently still a private R package on GitHub - under (re)development to accommodate modern formats for Agilent Cary UV-vis and Cytiva Äkta datafiles. Updates expected fall 2024.