Kalan-Lab

All

18 repositories

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 Mar 10, 2026Mar 10, 2026
zol
Public
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
visualization bioinformatics genomics
visualization bioinformatics genomics evolution detection metagenomics comparative-genomics phage gene-clusters bgc
Python
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BSD 3-Clause "New" or "Revised" License
•5•71•2•0•Updated Mar 9, 2026Mar 9, 2026
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
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 Jan 19, 2026Jan 19, 2026
Ancestral_BGC_Exansions_Study
Public
Code and datasets for analyses featured in Salamzade, Kalan, and Currie, 2025
HTML
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Dec 17, 2025Dec 17, 2025
lsaBGC-Pan
Public
lsaBGC - suite for pan-BGC-omics analysis
genomics evolution comparative-genomics
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•23•2•0•Updated Nov 21, 2025Nov 21, 2025
lsaBGC
Public
lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters
bioinformatics genomics bgc
bioinformatics genomics bgc biosynthetic-gene-clusters evolutionary-analysis
Python
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BSD 3-Clause "New" or "Revised" License
•4•41•0•0•Updated Sep 28, 2025Sep 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 antisept…
R
•0•0•0•0•Updated Jun 27, 2025Jun 27, 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 th…
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 …
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 promot…
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…
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 mur…
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