Kalan-Lab

All

18 repositories

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-transfer phage gene-clusters codon-usage biosynthetic-gene-clusters mobile-genetic-elements
Python
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BSD 3-Clause "New" or "Revised" License
•1•13•0•0•Updated Sep 15, 2025Sep 15, 2025
zol
Public
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
visualization bioinformatics genomics evolution detection metagenomics comparative-genomics phage gene-clusters bgc
Python
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BSD 3-Clause "New" or "Revised" License
•4•62•2•0•Updated Sep 8, 2025Sep 8, 2025
SkinBioassayStudy
Public
Code and data for Kalan lab skin bioassay project
R
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Sep 2, 2025Sep 2, 2025
Ancestral_BGC_Exansions_Study
Public
Code and datasets for analyses featured in Salamzade, Kalan, and Currie, 2025
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
lsaBGC-Pan
Public
lsaBGC - suite for pan-BGC-omics analysis
genomics evolution comparative-genomics biosynthetic-gene-clusters gene-cluster-families secondary-metabolism pan-genomics
Python
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BSD 3-Clause "New" or "Revised" License
•2•20•1•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
lsaBGC
Public
lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters
bioinformatics genomics bgc biosynthetic-gene-clusters evolutionary-analysis
Python
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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
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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
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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
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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
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Dec 14, 2022Dec 14, 2022