antimicrobial-resistance
There are 37 repositories under antimicrobial-resistance topic.
pha4ge/hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
phac-nml/staramr
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
nmquijada/tormes
Making whole bacterial genome sequencing data analysis easy
szczurek-lab/hydramp
HydrAMP: a deep generative model for antimicrobial peptide discovery
BorgwardtLab/maldi_amr
Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"
wanyuac/GeneMates
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
beiko-lab/arete
AMR/VF LGT focused bacterial genomics analysis workflow
pha4ge/hAMRonization_workflow
Harmonization of AMR predictor tool outputs
cidgoh/GRDI_AMR_One_Health
A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
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
jhayer/baargin
Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow
oxfordmmm/gnomonicus
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
joelewis101/blantyreESBL
Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi
AClark-WHONET/AMRIE
Antimicrobial Resistance Test Interpretation Engine
aryanGupta-09/AMROrbit
An antimicrobial resistance (AMR) dashboard.
divprasad/1DconvKernels
👨💻🧬🤖 deep neural networks: 1Dconvolution experiments with kernel size and stride length
M-Serajian/MTB-Pipeline
MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.
oxfordmmm/AMR-catalogue-demo
A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues
ReemaSingh/Mtb_Reoccurence_WGS
Bioinformatics analysis used to determine reinfection and relapse tuberculosis using whole genome sequencing data.
wanyuac/NITREc
Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli
wanyuac/PAMmaker
Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results
dachbrown/dissertation-bioinformatics-machine-learning
Collection of planning documents, visualizations, and presentations for my dissertation research. "Investigating Multidrug Resistance in Escherichia coli with Phylogenetics and Machine Learning"
palazzilorenzo/synthetic-data-for-antimicrobial-resistance
Conditional Variational Auto-Encoder for generation of synthetic data for Antimicrobial Resistance.
rretkute/AMbeRland
Analysis and visualisation of antimicrobial resistance
ShwetaNagre/MIP_ORACLE
MIP_ORACLE: Identifies unique target regions with diagnostic significance in pathogens.
srikanth-srinvas/ARG-Mapper
A standardized Python pipeline for comparative analysis of antibiotic resistance genes (ARGs) in bacterial genomes.
vsmicrogenomics/AMRFinderPlus-Matrix
AMRFinderPlus-Matrix contains script for processing the output files of AMRFinderPlus and generating a binary matrix that shows the presence or absence of antibiotic resistance genes, stress response genes, and virulence genes in each sample.
BCCDC-PHL/mykrobe-nf
Nextflow Wrapper for Mykrobe
dfornika/amrhike
Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
dinesh2k19/amr
In this repository, we have compiled the WGS analysis schematics of the bacterial isolates obtained from poultry manure of layer and broiler poultry farms
mcavallaro/ML4AMR
Software supporting M. Cavallaro, et al., Informing antimicrobial stewardship with explainable AI. PLOS Digit Health 2(1): e0000162 (2023) https://doi.org/10.1371/journal.pdig.0000162
Public-Health-Bioinformatics/irida-plugin-resistance-screen
Detect the presence of specific resistance genes in a sample using the IRIDA system
wanyuac/ARIBA_toolkit
Scripts for ARIBA-based gene detection