antibiotic-resistance

There are 3 repositories under antibiotic-resistance topic.

• ncbi / amr

  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

  antibiotic-resistancebioinformaticsgenomicspathogen
  Language:C++ 242

• will-rowe / groot

  A resistome profiler for Graphing Resistance Out Of meTagenomes

  alignmentantibiotic-resistancelshmetagenomicsminhashresistome
  Language:Go 63

• nf-core / funcscan

  (Meta-)genome screening for functional and natural product gene sequences

  nextflowworkflowpipelineassemblycontigsfunctionscreeningmetagenomicsnatural-productsantimicrobial-resistance-genesantimicrobial-peptidesbiosynthetic-gene-clustersbioinformaticsampantibiotic-resistanceargbgcsecondary-metabolitesamrnf-core
  Language:Nextflow 56

• pianpianyouche / plascad

  Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.

  plasmidsantibiotic-resistance
  Language:Python 37

• xinehc / args_oap

  ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database

  antibiotic-resistanceantibioticsmetagenomics
  Language:Python 32

• caozhichongchong / arg_ranker

  antibiotic-resistancerisk-assessmentmetagenomics
  Language:Python 22

• BigDataBiology / argNorm

  ARG normalization by mapping to the ARO ontology.

  antibiotic-resistancebioinformatics
  Language:Python 16

• dmnfarrell / pathogenie

  Desktop tool for microbial genome annotation and gene detection

  amrantibiotic-resistancebioinformaticsgenome-annotationgenomicspyqt5
  Language:Jupyter Notebook 12

• aldro61 / patric_tools

  Python package to interact with the PATRIC database (https://www.patricbrc.org)

  antibiotic-resistancedatabasegenomicspatric
  Language:Jupyter Notebook 9

• KiranJavkar / PRAWNS

  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

  population-genomicscomparative-genomicswhole-genome-genotypingpan-genome-analysisbioinformaticsgenomicscomputational-biologyantimicrobial-resistancebacterial-gwasantibiotic-resistancewhole-genome-sequencingwhole-genome-alignmentgenome-analysisparallel-programmingassociation-studiesmicrobial-genomics
  Language:C++ 7

• gaarangoa / ARGminer

  Curation of Antibiotic Resistance Genes by using crowdsourcing

  antibiotic-resistancecrowdsourcingdatabase
  Language:CSS 6

• gaarangoa / ExtrARG

  Extract discriminatory ARGs from metagenomics samples

  antibiotic-resistancemetagenomicsngs
  Language:Python 5

• aldro61 / kover2_paper

  Interpretable genotype-to-phenotype models with rule-based classifiers

  antibiotic-resistancegenomicsmachine-learning
  Language:Python 4

• CaileanCarter / AbxRxPro

  Visualise your isolate's antibiotic resistance profile

  amrantibiotic-resistance
  Language:Python 4

• KarolinaGustavsson / Antibiotics_Chemprop

  Antibiotic discovery using graph deep learning, with Chemprop.

  machine-learninggraph-deep-learningchempropantibiotic-resistance
  Language:Python 4

• joycewang914 / Genomic_and_Patient_Transfer_Analyasis_of_Resistant_Bacteria

  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.

  transmissiongenomic-data-analysisgenomics-visualizationmicrobial-genomicsepidemiologyantibiotic-resistancenursingsurveillancecolonizationjournal-article
  Language:R 3

• ryansmcgee / pycrobe

  A simple package for simulations of microbial growth experiments with realistic sources of error.

  antibiotic-resistancebacterial-samplesexperimental-evolutiongrowth-curve-modelsmicrobial-communitiesmicrobial-ecologymicrobial-evolution
  Language:Python 2

• Anna-Pico / Antibiotic-resistance-genes-in-metagenomes---TFM

  This Github repository contains the files used to perform a master thesis about antibiotic resistance genes in wastewater.

  antibiotic-resistanceargdiamondfastq-filesfastx-toolkitgenomicsmetagenomicsmetaxa
  Language:R 1

• AstraBert / resistML

  A tool for AMR gene family prediction, simple and ML-based

  aiantibiotic-resistancebert-modelfinetuninghealthcaremachine-learningprotein-sequencestext-classificationvoting-classifier
  Language:Jupyter Notebook 1

• BCCDC-PHL / plasmid-screen

  Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite

  bioinformatics-pipelineplasmidsantibiotic-resistancegenomic-epidemiology
  Language:Python 1
• multi-resistance

  dannagifford / multi-resistance

  Data, source code and scripts for BIORXIV/2019/643585v3

  evolutionantibiotic-resistancesimulation-modelingstochastic-modellingbayesian-inference
  Language:R 1

• davidegat / GameOfBacteria

  An educational simple game in Italian/English that simulates interaction between antbiotics and bacteria.

  antibiotic-resistanceantibioticsbacteriaeducational-gamegamelearningpygamepythonteachersteaching-materialsvideogameai-assisted-developmentai-codedai-generatedai-musicmedicalsimulationsimulator
  Language:Python 1

• joycewang914 / Microbial_Antibiotic_Network_in_Nursing_Homes

  Interaction networks between antibiotic exposure, microbial factors and clinical features in nursing home patients influence the risk of catheter-associated urinary tract infection.

  antibiotic-resistancenursinginfection-controlnetwork-analysisjournal-articler
  Language:R 1

• joycewang914 / Nursing_Home_Patient_Gut_Microbiota

  Identifying gut microbiome features associated with the risk of acquiring an enteric drug-resistant organism (e.g. vancomycin-resistant Enterococcus and resistant gram-negative bacteria) in patients recently discharged from acute-care hospital and admitted into nursing homes.

  nursingantibiotic-resistancemicrobiome-analysismothurantibiotic-stewardshipjournal-article
  Language:R 1

• Kronopt / SimulATe

  Simulator of Antibiotic Therapy Effects on the Dynamics of Bacterial Populations

  pythonpython-2kivyantibiotic-resistancebacteriamicrobiomeenterotypesimulation
  Language:Python 1

• lasupernova / AMR_chatbot

  Natural language processing chatbot answering questions about antibiotics and antibiotic resistance

  nlpnatural-language-processingamrantibiotic-resistancenltk
  Language:Python 1

• NewtonLabUWM / DrinkingWaterPipe_Ecology

  Data and code for Kimbell et al., 2021

  drinking-watermicrobial-ecologymicrobial-communities16s-rrnaantibiotic-resistancemilwaukee
  Language:R 1

• ZiemertLab / ARTS

  Antibiotic Resistant Target Seeker (ARTS)

  antibiotic-resistancegenome-miningresistance-based-genome-miningbioinformatics
  Language:Python 1

• AmyOBro / MScProject

  An examination of genomic resistance and virulence of Escherichia marmotae dentified in deer faeces Portumna, Galway.

  antibiotic-resistanceescherichiaone-healthvirulence-genes
  Language:Shell 0

• davidegat / AntibiogramSimulator

  A simple simulator that shows the easy way how an antibiogram works

  ai-assisted-developmentai-codedai-generatedai-musicantibiotic-resistanceantibioticsbacteriaeducational-gamegamelearningmedicalpygamepythonsimulationsimulatorteachersteaching-materialsvideogame
  Language:Python 0

• jeremyboyd / Idaho-antibiotic-use

  Project that estimates the use and overuse of antibiotics in Idaho based on Medicare Part D data.

  antibiotic-resistanceantibioticsidahomedicare-data
  Language:CSS 0

• kenan-erol / MicrobeClassification

  Classification model predicting the type of microbe from provided features

  antibiotic-resistanceartificial-intelligencebacteriadata-sciencegenomesmicrobes
  Language:Jupyter Notebook 0

• nali321 / metabundance

  Metabundance: Investigating ARG abundance in metagenomes and linking them to MGEs

  antibiotic-resistancebioinformaticsmetagenomicsmobile-genetic-elementspipelinesnakemake
  Language:Python 0

• geovalexis / ml-in-args

  Early prediction of Antimicrobial Resistance (AMR) using Machine Learning

  antibiotic-resistancebioinformaticsdata-sciencemachine-learning
  Language:Jupyter Notebook

• jvelezmagic / undergraduate_research_project

  rbookdownbacteriaantibiotic-resistanceunamfilamentationcell-tracking
  Language:TeX

• Romaric1331 / Artistic-Project-with-Genome-Music

  This is an interdisciplinary team project with Life Sci, Learning Sci, Digital Sci and FIRE tracks for showing the influence of Antibiotics Resistance from Learning Planet Institute- Université Paris Cité

  antibiotic-resistanceartgenome-musicpython
  Language:Jupyter Notebook