The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.
☆73Sep 1, 2022Updated 4 years ago
Alternatives and similar repositories for microbiomeExplorer
Users that are interested in microbiomeExplorer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A comprehensive R package for deep mining microbiome☆195Apr 29, 2026Updated 5 months ago
- A collection of python and bash scripts for various bioinformatics-related tasks☆13Sep 19, 2024Updated 2 years ago
- Visualize microbiome data with black magic ggtree☆67Sep 3, 2020Updated 6 years ago
- Dadaist2 🟨 Highway to R☆13Mar 7, 2025Updated last year
- A list of R environment based tools for microbiome data exploration, statistical analysis and visualization☆117Apr 11, 2023Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- A companion R package for the MicrobiomeAnalyst web server☆132Sep 29, 2026Updated last week
- An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…☆34Nov 12, 2020Updated 5 years ago
- A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.☆466Feb 13, 2026Updated 7 months ago
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Oct 29, 2025Updated 11 months ago
- bioBakery tools for meta'omic profiling☆323Aug 4, 2026Updated 2 months ago
- R package for microbiome biomarker discovery☆199Feb 19, 2025Updated last year
- An R package for microbial community analysis in an environmental context☆67Sep 23, 2020Updated 6 years ago
- Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…☆26Aug 20, 2026Updated last month
- Analysing Metagenomic Species (MGS)☆41Nov 12, 2020Updated 5 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Snakemake pipeline for amplicon sequencing using dada2☆10Jul 17, 2023Updated 3 years ago
- strain-level analysis tools☆40Oct 21, 2024Updated last year
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated last year
- A tool for removing redundant genomes from a set of assemblies☆86Jul 24, 2026Updated 2 months ago
- hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis☆71Feb 9, 2025Updated last year
- A hybrid assembly and MAG recovery pipeline (and more!)☆120Updated this week
- phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; an…☆651Feb 27, 2026Updated 7 months ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆71Aug 10, 2021Updated 5 years ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A model-based visualization method for microbiome data☆16Jul 17, 2026Updated 2 months ago
- A logistic regression model for testing differential abundance in compositional microbiome data☆13Jul 25, 2023Updated 3 years ago
- Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…☆61Jun 11, 2022Updated 4 years ago
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆253Sep 24, 2026Updated 2 weeks ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆26Jul 22, 2024Updated 2 years ago
- Protocols, data and code associated with the MK-SpikeSeq method for quantifying the absolute abundances of microbiota samples☆12May 19, 2021Updated 5 years ago
- ATLAS - Three commands to start analyzing your metagenome data☆405May 28, 2026Updated 4 months ago
- diversity estimation under ecological networks☆83Jun 16, 2026Updated 3 months ago
- Count and compare 16S rRNA genes within a genus☆17Aug 1, 2024Updated 2 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- ⚡🦠🧬📇 Rapid microbial genomes-to-report pipeline☆75Sep 23, 2026Updated 2 weeks ago
- ☆65Oct 2, 2026Updated last week
- Prediction of microbial interactions in complex communities☆14Aug 14, 2024Updated 2 years ago
- Pipeline for major biological analyses.☆35Mar 30, 2022Updated 4 years ago
- Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project☆12May 25, 2022Updated 4 years ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆17May 18, 2020Updated 6 years ago
- Statistics and visualization for amplicon data☆74May 21, 2026Updated 4 months ago