AClark-WHONET/AMRIE

Antimicrobial Resistance Test Interpretation Engine

Language: C# - Size: 1.2 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 1 - Forks: 1

beiko-lab/arete

AMR/VF LGT focused bacterial genomics analysis workflow

Language: Python - Size: 36.7 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 19 - Forks: 4

oxfordmmm/gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

Language: Python - Size: 4.24 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 5 - Forks: 0

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.

Size: 160 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 6 - Forks: 0

jhayer/baargin

Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow

Language: Nextflow - Size: 15.3 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 6 - Forks: 0

phac-nml/staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Language: Python - Size: 9.3 MB - Last synced: 22 days ago - Pushed: 9 months ago - Stars: 103 - Forks: 25

BCCDC-PHL/mykrobe-nf

Nextflow Wrapper for Mykrobe

Language: Python - Size: 3.91 KB - Last synced: 29 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

Public-Health-Bioinformatics/irida-plugin-resistance-screen

Detect the presence of specific resistance genes in a sample using the IRIDA system

Language: Java - Size: 973 KB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 2

Public-Health-Bioinformatics/irida-plugin-tbprofiler

Language: Java - Size: 410 KB - Last synced: 29 days ago - Pushed: 8 months ago - Stars: 1 - Forks: 1

dfornika/amrhike

Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike

Language: Clojure - Size: 13.7 KB - Last synced: 29 days ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

pha4ge/hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Language: Python - Size: 5.39 MB - Last synced: 29 days ago - Pushed: 7 months ago - Stars: 113 - Forks: 24

szczurek-lab/hydramp

HydrAMP: a deep generative model for antimicrobial peptide discovery

Language: Jupyter Notebook - Size: 1.42 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 27 - Forks: 8

pha4ge/hAMRonization_workflow

Harmonization of AMR predictor tool outputs

Language: Python - Size: 1.44 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 20 - Forks: 8

numpde/counter-resistance

Language: TypeScript - Size: 1.15 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

palazzilorenzo/synthetic-data-for-antimicrobial-resistance

Conditional Variational Auto-Encoder for generation of synthetic data for Antimicrobial Resistance.

Language: Python - Size: 283 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

M-Serajian/MTB-plus-plus

MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.

Language: Python - Size: 16.3 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

joelewis101/blantyreESBL

Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi

Language: R - Size: 243 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 3 - Forks: 0

nmquijada/tormes

Making whole bacterial genome sequencing data analysis easy

Language: Shell - Size: 51 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 87 - Forks: 31

wanyuac/GeneMates

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences

Language: R - Size: 2.4 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 22 - Forks: 2

BorgwardtLab/maldi_amr

Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"

Language: Jupyter Notebook - Size: 2.52 GB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 20 - Forks: 9

aldro61/kb_kover_amr

Antimicrobial resistance prediction app for KBase

Language: Python - Size: 5.26 MB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 2

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"

Language: Shell - Size: 10.8 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

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.

Language: Python - Size: 31.3 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

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

Language: C++ - Size: 6.7 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 6 - Forks: 1

oxfordmmm/AMR-catalogue-demo

A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues

Language: Jupyter Notebook - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

wanyuac/NITREc

Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli

Language: Python - Size: 146 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

mcavallaro/ML4AMR

Language: Jupyter Notebook - Size: 721 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

wanyuac/ARIBA_toolkit

Scripts for ARIBA-based gene detection

Language: Python - Size: 34.2 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

wanyuac/PAMmaker

Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results

Language: Python - Size: 88.9 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

divprasad/1DconvKernels

👨‍💻🧬🤖 deep neural networks: 1Dconvolution experiments with kernel size and stride length

Language: Jupyter Notebook - Size: 42.8 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

Public-Health-Bioinformatics/irida-plugin-plasmid-screen

Language: Java - Size: 769 KB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

rretkute/AMbeRland

Analysis and visualisation of antimicrobial resistance

Language: R - Size: 222 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0