Repositories list

• Ancestral_BGC_Exansions_Study

  Public
  Code and datasets for analyses featured in Salamzade, Kalan, and Currie, 2024.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

• zol

  Public
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

  visualizationbioinformaticsgenomics+ 9evolutiondetectionmetagenomicscomparative-genomicsphagegene-clustersbgc+ 2

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •4•61•1•0•Updated Jul 29, 2025Jul 29, 2025

• lsaBGC-Pan

  Public
  lsaBGC - suite for pan-BGC-omics analysis

  genomicsevolutioncomparative-genomics+ 4biosynthetic-gene-clustersgene-cluster-familiessecondary-metabolismpan-genomics

  Python

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  BSD 3-Clause "New" or "Revised" License

  •2•19•1•0•Updated Jul 28, 2025Jul 28, 2025

• codoff

  Public
  codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the full genome.

  horizontal-gene-transferphagegene-clusters+ 3codon-usagebiosynthetic-gene-clustersmobile-genetic-elements

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•12•0•0•Updated Jul 28, 2025Jul 28, 2025

• Townsend_etal_ExVivoPorcineSkinCHG

  Public
  Code for data analysis and figures for the manuscript Establishing an ex vivo porcine skin model to investigate the effects of chlorhexidine gluconate antiseptic on viable skin microbial communities."

  R

  •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

• SkinBioassayStudy

  Public
  Code and data for Kalan lab skin bioassay project

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

• lsaBGC

  Public
  lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

  bioinformaticsgenomicsbgc+ 2biosynthetic-gene-clustersevolutionary-analysis

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •4•37•0•0•Updated Apr 19, 2025Apr 19, 2025

• Salamzade_Kalan_BGC_Evolution_Review

  Public
  Code for small (re-)analyses for the Salamzade & Kalan minireview on BGC evolution

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• Salamzade_etal_zol

  Public
  Misc. code & scripts associated with the zol & fai manuscript.

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

• Bioassay-ML-Image-Classification

  Public
  This repository contains a script for training a machine learning model to classify images into categories. The model is trained on custom images provided by the user.

  Jupyter Notebook

  •0•1•0•0•Updated Aug 2, 2024Aug 2, 2024

• DeLaCruz_Townsend_etal_PorcineSkinMicrobiome

  Public
  Code for data analysis and figures for the manuscript "Discovering the Microbial Community and Antifungals within the Porcine Skin Microbiome" by K. De La Cruz and E.C. Townsend et al.

  R

  •0•0•0•0•Updated Apr 30, 2024Apr 30, 2024

• Townsend_etal_StillNotSterile

  Public
  Code for data analysis and figures for the manuscript "Still Not Sterile: Chlorhexidine gluconate does not completely reduce skin microbial bioburden and promotes pathogen overabundance in patients undergoing elective surgeries" by E.C. Townsend et al.

  R

  •0•0•0•0•Updated Apr 11, 2024Apr 11, 2024

• Townsend_etal_WhatIsSlough

  Public
  Code for data analysis and figures for the manuscript "What is Slough? Defining the proteomic and microbial composition of wound slough and its implications for wound healing" by E.C. Townsend et al.

  R

  •0•0•0•0•Updated Jan 30, 2024Jan 30, 2024

• Spurgeon_Townsend_etal_MmuPV1_VaginalMicrobiome

  Public
  Code for data analysis and figures for the manuscript "Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model" by M.E. Spurgeon and E.C. Townsend et al.

  R

  •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

• Swaney_etal_CobamidePaper

  Public
  Code for data analysis and visualization in Swaney et al. mSystems 2022

  R

  •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023

• Swaney_etal_SkinMediaPaper

  Public
  Code for data analysis and visualization in Swaney et al. Microbiology Spectrum 2023

  R

  •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023

• lsaBGC_Ckefir_Testing_Cases

  Public
  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 16, 2023Jan 16, 2023

• Salamzade_etal_CtuberCompGen

  Public
  Code for Comparative Genomics + Metagenomic Investigation of the C. tuberculostearicum species complex

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 14, 2022Dec 14, 2022