Three bacterial GWAS methods all rolled into one easy-to-use R package
☆22Apr 16, 2024Updated 2 years ago
Alternatives and similar repositories for hogwash
Users that are interested in hogwash are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Feb 6, 2018Updated 8 years ago
- A tooL for Prokaryotic Phylogeny And Clustering Analysis☆13Jul 28, 2025Updated 9 months ago
- A nextflow pipeline for performing bacterial RNA-Seq data analysis.☆13Apr 26, 2026Updated 2 weeks ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Feb 6, 2025Updated last year
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14May 12, 2024Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Feb 12, 2016Updated 10 years ago
- scRNA-seq Shiny App☆14May 1, 2023Updated 3 years ago
- Bact-Builder: Microbial de novo genome assembly pipeline☆13Dec 5, 2022Updated 3 years ago
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆10Jun 13, 2023Updated 2 years ago
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆41Dec 8, 2022Updated 3 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Apr 11, 2018Updated 8 years ago
- Nucmer from Mummer3 followed by ggplot for nicer and more customisable genome alignment plots.☆11Feb 25, 2021Updated 5 years ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Pan-genome wide association studies☆216May 29, 2024Updated last year
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆121May 21, 2024Updated last year
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆133Feb 26, 2024Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated 2 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated 2 years ago
- R codes and data for 'Smoking, Alcohol consumption, and 24 Gastrointestinal Diseases: Mendelian Randomization Analysis'☆11Mar 5, 2023Updated 3 years ago
- Gene Absence Presence Identification tool.☆27Mar 28, 2025Updated last year
- ☆12Dec 4, 2023Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- strain-level analysis tools☆39Oct 21, 2024Updated last year
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)☆52Dec 22, 2024Updated last year
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆124Aug 24, 2023Updated 2 years ago
- "Reads to report" for public health and clinical microbiology☆143Dec 9, 2025Updated 5 months ago
- An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests☆14May 27, 2025Updated 11 months ago
- HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.☆44Feb 11, 2023Updated 3 years ago
- Within-species genome-wide dN/dS estimation from very many genomes☆23Oct 26, 2020Updated 5 years ago
- Identify phage regions in bacterial genomes for masking purposes☆33Sep 5, 2019Updated 6 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- transposable element typing pipeline☆19Mar 8, 2024Updated 2 years ago
- ☆38Apr 14, 2022Updated 4 years ago
- Code to run Mendelian Randomization Analysis☆10Mar 14, 2022Updated 4 years ago
- A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes☆18Dec 1, 2025Updated 5 months ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- SEER, reimplemented in python 🐍🔮☆133Mar 24, 2026Updated last month
- ☆16Dec 7, 2020Updated 5 years ago