ncbi/amr

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

Language: C++ - Size: 2.01 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 242 - Forks: 33

nf-core/funcscan

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

Language: Nextflow - Size: 12.9 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 56 - Forks: 17

shliamin/Python-Genome-Assembler

This repository contains a Python-based genome assembler designed to perform k-mer spectrum-based error correction and generate SAM files for visualizing genome mappings. It supports genomic data analysis with a focus on identifying mutations relevant to antibiotic resistance.

Language: Python - Size: 542 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

dmnfarrell/pathogenie

Desktop tool for microbial genome annotation and gene detection

Language: Jupyter Notebook - Size: 30.3 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 12 - Forks: 4

tvlpirb/gcb-antibiotics-sim

Simulating antibiotic resistant bacteria growth

Language: Jupyter Notebook - Size: 14.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

BCCDC-PHL/plasmid-screen

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

Language: Python - Size: 51.8 KB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

gaarangoa/argpore-cli

Client Serive of ARGpore pipeline for the analysis of antibiotic resistance in nanopore reads

Language: CSS - Size: 7.84 MB - Last synced: about 2 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

BigDataBiology/argNorm

ARG normalization by mapping to the ARO ontology.

Language: Python - Size: 12.1 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 14 - Forks: 3

pianpianyouche/plascad

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

Language: Python - Size: 10.8 MB - Last synced: 21 days ago - Pushed: over 3 years ago - Stars: 37 - Forks: 11

AstraBert/resistML

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

Language: Jupyter Notebook - Size: 1.54 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

nali321/metabundance

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

Language: Python - Size: 1.96 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

xinehc/args_oap

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

Language: Python - Size: 87.3 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 27 - Forks: 10

ZiemertLab/ARTS

Antibiotic Resistant Target Seeker (ARTS)

Language: Python - Size: 123 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

davidegat/GameOfBacteria

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

Language: Python - Size: 36 MB - Last synced: 5 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

caozhichongchong/arg_ranker

Language: Python - Size: 96.1 MB - Last synced: 12 days ago - Pushed: 5 months ago - Stars: 22 - Forks: 11

geovalexis/ml-in-args

Early prediction of Antimicrobial Resistance (AMR) using Machine Learning

Language: Jupyter Notebook - Size: 16.9 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

davidegat/AntibiogramSimulator

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

Language: Python - Size: 2.11 MB - Last synced: 5 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

will-rowe/groot

A resistome profiler for Graphing Resistance Out Of meTagenomes

Language: Go - Size: 12.5 MB - Last synced: 8 months ago - Pushed: about 4 years ago - Stars: 61 - Forks: 6

aldro61/patric_tools

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

Language: Jupyter Notebook - Size: 56.6 KB - Last synced: 8 months ago - Pushed: over 4 years ago - Stars: 9 - Forks: 4

lasupernova/AMR_chatbot

Natural language processing chatbot answering questions about antibiotics and antibiotic resistance

Language: Python - Size: 205 KB - Last synced: 8 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

CaileanCarter/AbxRxPro

Visualise your isolate's antibiotic resistance profile

Language: Python - Size: 416 KB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0

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

Language: Jupyter Notebook - Size: 19 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

FAIMS/scoop-a-poop

Citizen science project investigating antibiotic resistance in wildlife. A collaboration between Macquarie University, Taronga Zoo and University of Sydney

Language: Java - Size: 1.5 MB - Last synced: 10 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

aldro61/kover2_paper

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

Language: Python - Size: 166 MB - Last synced: 11 months ago - Pushed: almost 4 years ago - Stars: 4 - Forks: 1

aldro61/kb_kover_amr

Antimicrobial resistance prediction app for KBase

Language: Python - Size: 5.26 MB - Last synced: 11 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 2

jaeihn/AntibioticResistanceSimulation

Java simulation of antibiotic resistance. Pretty cute.

Language: Java - Size: 1.01 MB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

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.

Language: R - Size: 207 KB - Last synced: 12 months ago - Pushed: almost 4 years ago - Stars: 1 - 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: over 1 year ago - Pushed: over 1 year ago - Stars: 6 - Forks: 1

Kronopt/SimulATe 📦

Simulator of Antibiotic Therapy Effects on the Dynamics of Bacterial Populations

Language: Python - Size: 881 KB - Last synced: over 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

gaarangoa/ARGminer

Curation of Antibiotic Resistance Genes by using crowdsourcing

Language: CSS - Size: 216 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 6 - Forks: 2

KarolinaGustavsson/Antibiotics_Chemprop

Antibiotic discovery using graph deep learning, with Chemprop.

Language: Python - Size: 372 KB - Last synced: over 1 year ago - Pushed: about 2 years ago - Stars: 3 - Forks: 2

kenan-erol/MicrobeClassification

Classification model predicting the type of microbe from provided features

Language: Jupyter Notebook - Size: 1.18 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

jeremyboyd/Idaho-antibiotic-use

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

Language: CSS - Size: 400 KB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

AmyOBro/MScProject

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

Language: Shell - Size: 28.3 KB - Last synced: over 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

jvelezmagic/undergraduate_research_project

Language: TeX - Size: 34.2 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

Genomic-Medicine-Linkoping/JASEN Fork of genomic-medicine-sweden/JASEN

Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

Language: Python - Size: 112 MB - Last synced: over 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

jvelezmagic/undergraduate_research_project3

Language: TeX - Size: 81.2 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

dannagifford/multi-resistance

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

Language: R - Size: 185 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

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.

Language: R - Size: 30.3 KB - Last synced: 12 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

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.

Language: R - Size: 9.58 MB - Last synced: 12 months ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 0

Genomic-Medicine-Linkoping/var-genes-ro

Virulence and Antibiotic Resistance Genes used with JASEN pipeline at the university hospital of Linköping, Sweden.

Language: Jupyter Notebook - Size: 506 KB - Last synced: 5 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

gaarangoa/ExtrARG

Extract discriminatory ARGs from metagenomics samples

Language: Python - Size: 297 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 5 - Forks: 1

NewtonLabUWM/DrinkingWaterPipe_Ecology

Data and code for Kimbell et al., 2021

Language: R - Size: 3.42 MB - Last synced: over 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1

crsl4/staph-visa

Reproducible scripts for the Su et al (2020) paper.

Size: 10.7 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

IBPA/OPEX

An optimal experimental design framework for accelerating knowledge discovery using gene expression data

Language: R - Size: 2.36 MB - Last synced: 3 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

ryansmcgee/pycrobe

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

Language: Python - Size: 247 KB - Last synced: 29 days ago - Pushed: over 4 years ago - Stars: 2 - Forks: 2

hossainlab/ARGs

Antibiotic Resistance Genes Finding

Language: Jupyter Notebook - Size: 1.73 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

chris-rands/annotated_profile_HMMs

Sets of protein familes represented as profile HMMs annotated for antibiotic resistance and virulence function.

Size: 7.51 MB - Last synced: over 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

boulund/armen

Antibiotic Resistance in Metagenomes

Language: Python - Size: 10.7 KB - Last synced: 8 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0