Code repository for machine learning and computational analysis of large-scale microbial genomics data (https://rdcu.be/9rHj)
☆20May 12, 2025Updated 9 months ago
Alternatives and similar repositories for microbial_AMR_ML
Users that are interested in microbial_AMR_ML are comparing it to the libraries listed below
Sorting:
- A flux balance analysis machine learning classifier for microbial GWAS☆14Jan 14, 2020Updated 6 years ago
- A library of Machine Learning tools to predict antibiotic resistance from NGS data☆18May 30, 2022Updated 3 years ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated last year
- A nextflow pipeline for performing bacterial RNA-Seq data analysis.☆12Oct 14, 2025Updated 4 months ago
- DarkHorse2 source code☆10May 3, 2022Updated 3 years ago
- Program for finding horizontal gene transfer using BLAST result☆11May 26, 2023Updated 2 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Sep 27, 2025Updated 5 months ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Apr 11, 2018Updated 7 years ago
- VESPA: Very large-scale Evolutionary and Selective Pressure Analyses☆15Mar 18, 2022Updated 3 years ago
- Program for estimating dN/dS in overlapping genes (OLGs)☆14Dec 2, 2022Updated 3 years ago
- ☆13Sep 4, 2017Updated 8 years ago
- PanGenomePipeline☆16Apr 10, 2024Updated last year
- Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA☆17Feb 29, 2024Updated 2 years ago
- The BV-BRC Command Line Interface☆17Aug 6, 2025Updated 6 months ago
- Code for doing MIC predictions on genomes☆41Dec 5, 2019Updated 6 years ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Feb 12, 2016Updated 10 years ago
- Create your own PanViz visualizations☆21Nov 20, 2017Updated 8 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆131Feb 26, 2024Updated 2 years ago
- Identify phenotype-specific k-mers and predict phenotype using sequenced bacterial strains☆21Jan 5, 2026Updated last month
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆105Jan 22, 2026Updated last month
- ☆26Feb 24, 2026Updated last week
- Mycobacterium tuberculosis next generation sequence analysis☆24Oct 11, 2019Updated 6 years ago
- Gene Absence Presence Identification tool.☆27Mar 28, 2025Updated 11 months ago
- A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets☆31Nov 9, 2025Updated 3 months ago
- ☆16Aug 17, 2023Updated 2 years ago
- xOmicsShiny: an R Shiny application for cross-omics data analysis and pathway mapping, Bioinformatics Advances, Volume 5, Issue 1, 2025, …☆38Feb 6, 2026Updated 3 weeks ago
- This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion☆21Mar 22, 2021Updated 4 years ago
- NCBI Prokaryotic Genome Annotation Pipeline☆369Feb 9, 2026Updated 3 weeks ago
- ☆136Updated this week
- a pipeline to process data of PEM-seq or data similar, which is more comprehensive than superQ☆10Feb 24, 2026Updated last week
- we collected Gram-stained bacteria images from lower respiratory tract specimens of patients with lung infections in Chinese PLA General…☆12Jan 18, 2024Updated 2 years ago
- HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high…☆10Apr 15, 2025Updated 10 months ago
- Horizontal gene transfer (HGT) identification pipeline☆69May 17, 2023Updated 2 years ago
- An interactive web-tool for RNA-seq analysis☆70Feb 12, 2026Updated 2 weeks ago
- IslandPath standalone software☆36Nov 7, 2023Updated 2 years ago
- CRyPTIC data processing pipelines☆34Jul 18, 2024Updated last year
- ☆39Jul 5, 2023Updated 2 years ago
- A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genom…☆29Oct 29, 2025Updated 4 months ago