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bioassay-ml-image-classification

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.

codoff

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

delacruz_townsend_etal_porcineskinmicrobiome

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.

lsabgc

lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

lsabgc-pan

lsaBGC - suite for pan-BGC-omics analysis

lsabgc_ckefir_testing_cases

salamzade_etal_ctubercompgen

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

salamzade_etal_zol

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

spurgeon_townsend_etal_mmupv1_vaginalmicrobiome

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.

swaney_etal_cobamidepaper

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

swaney_etal_skinmediapaper

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

townsend_etal_stillnotsterile

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.

townsend_etal_whatisslough

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.

zol

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