Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
☆114Sep 4, 2026Updated this week
Alternatives and similar repositories for AMR
Users that are interested in AMR are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- R Package for Data-Driven Antimicrobial Stewardship & Surveillance in Hospitals☆12May 11, 2024Updated 2 years ago
- A flexible pipeline for complete analysis of bacterial genomes☆523Aug 5, 2026Updated last month
- Minimum Bait Cover Toolkit Syotti.☆15Jan 22, 2025Updated last year
- R implementation of the LEfSe method☆67May 14, 2026Updated 3 months ago
- Profiler for metagenomics based on NGLess☆14Feb 22, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.☆129Jul 28, 2026Updated last month
- The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimic…☆20Jul 30, 2026Updated last month
- functions for analyzing phyloseq data☆28Feb 4, 2025Updated last year
- ☆25Jul 28, 2025Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆28May 7, 2026Updated 4 months ago
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Apr 30, 2026Updated 4 months ago
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 4 years ago
- Small Helpers and Tricks for Epidemics Analysis☆12Sep 20, 2023Updated 2 years ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆182Aug 10, 2026Updated 3 weeks ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Bacterial taxonomy construction and evaluation in R☆16Jan 30, 2024Updated 2 years ago
- t-distributed stochastic neighbor embedding for microbiota data☆13May 12, 2019Updated 7 years ago
- ☆35Aug 28, 2025Updated last year
- Working with the outputs of sourmash in R☆29Jan 15, 2026Updated 7 months ago
- A quarto website for NHS-R Community☆13Aug 26, 2026Updated last week
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- Phylogenetic Organization of Metagenomic Signals (POMS)☆18Dec 19, 2022Updated 3 years ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆208Jun 10, 2026Updated 2 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆34Jul 17, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated 2 years ago
- Ying's tools for analysis, with particular focus on microbiome data☆40Jul 6, 2026Updated 2 months ago
- an example of building up a targets analysis for -omics data☆12Jun 23, 2023Updated 3 years ago
- Files for a minimal 'reproducible' PhD thesis☆11May 11, 2020Updated 6 years ago
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated 6 months ago
- MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-thro…☆26Nov 14, 2022Updated 3 years ago
- Convert dates to arbitrary week definitions☆17Oct 6, 2022Updated 3 years ago
- Plasmid exploration of bacterial genomes☆27Mar 2, 2022Updated 4 years ago
- ☆10Mar 24, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Generate de novo taxonomy of full length 16S rRNA sequences directly from environmental samples☆20Nov 23, 2024Updated last year
- Making whole bacterial genome sequencing data analysis easy☆115Apr 22, 2025Updated last year
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆183Apr 16, 2025Updated last year
- The Antibiotic Resistance Ontology (ARO) organizes the information describing the ability of a microorganism to withstand the effects of …☆22Aug 13, 2026Updated 3 weeks ago
- Slides and example code for debugging {targets} pipelines☆10Apr 17, 2025Updated last year
- CroCoDeEL detects cross-sample contamination in shotgun metagenomic data☆32Aug 28, 2026Updated last week
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 8 months ago