Python script to extract and visualize AMR data from AMRFinderPlus outputs, generating detailed reports and binary heatmaps
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Oct 23, 2024 - Python
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amrfinderplus
Here are 6 public repositories matching this topic...
AI-assisted pipeline for mining candidate Staphylococcus invasome and virulence-associated genes from assembled genome FASTA files.
python bash bioinformatics pipeline genomics reproducible-research conda virulence abricate staphylococcus bacterial-genomics bakta amrfinderplus invasome vfdb
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May 27, 2026 - Python
Characterising the AMR landscape via EDA and predictive modelling, and developing an integrated pipeline that bridges genomic surveillance data to protein targets and ligand candidates for downstream drug discovery.
machine-learning bioinformatics-pipeline drug-discovery molecular-modeling antimicrobial-resistance xgboost-classifier amrfinderplus
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Jun 2, 2026 - Jupyter Notebook
AMR prediction pipeline for Acinetobacter baumannii using whole-genome sequencing and machine learning (Random Forest, Logistic Regression) with SHAP-based gene importance analysis.
machine-learning logistic-regression feature-engineering genome-analysis antibiotics random-forest-classifier bacterial-genomes antimicrobial-resistance shap genome-features amrfinderplus resistance-phenotype
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May 22, 2026 - Jupyter Notebook
Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.
bioinformatics microbial-genomics comparative-genomics synteny phylogenomics pangenomics mafft resistome prokka fastani bacterial-genomics amrfinderplus iqtree2 helicobacter-pylori ppanggolin
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Apr 6, 2026 - Shell
Bioinformatic pipeline for prioritizing novel biosynthetic gene clusters (BGCs) from actinobacterial genomes against the MiBIG 4.0 reference space, with resistance-associated feature screening (Pfam domains and AMRFinderPlus).
antismash genome-mining natural-products actinobacteria biosynthetic-gene-clusters amrfinderplus bgc-prioritization bigscape mibig microbial-natural-products
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Jun 20, 2026 - Python
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