AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
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Updated
May 22, 2024 - C++
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
(Meta-)genome screening for functional and natural product gene sequences
Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.
ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
A resistome profiler for Graphing Resistance Out Of meTagenomes
Desktop tool for microbial genome annotation and gene detection
Python package to interact with the PATRIC database (https://www.patricbrc.org)
ARG normalization by mapping to the ARO ontology.
A simple package for simulations of microbial growth experiments with realistic sources of error.
Curation of Antibiotic Resistance Genes by using crowdsourcing
Antimicrobial resistance prediction app for KBase
Antibiotic discovery using graph deep learning, with Chemprop.
An optimal experimental design framework for accelerating knowledge discovery using gene expression data
Interpretable genotype-to-phenotype models with rule-based classifiers
Data and code for Kimbell et al., 2021
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
Extract discriminatory ARGs from metagenomics samples
PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features
Active surveillance of newly-admitted nursing home patients for colonization of antibiotic-resistant bacteria reveals that multiple lineages have spread across southeast Michigan healthcare networks.
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