phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
☆649Feb 27, 2026Updated 3 months ago
Alternatives and similar repositories for phyloseq
Users that are interested in phyloseq are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Accurate sample inference from amplicon data with single nucleotide resolution☆552Feb 13, 2026Updated 3 months ago
- microbiome R package☆316May 12, 2026Updated 2 weeks ago
- Code, unit tests, and tutorials for running PICRUSt2☆388Nov 27, 2025Updated 6 months ago
- Import qiime2 artifacts to R☆180Dec 12, 2024Updated last year
- A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.☆460Feb 13, 2026Updated 3 months 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.
- An R package for microbial community analysis in an environmental context☆67Sep 23, 2020Updated 5 years ago
- A companion R package for the MicrobiomeAnalyst web server☆132May 22, 2026Updated last week
- Statistical analysis for sparse high-throughput sequencing☆73Dec 17, 2024Updated last year
- Rachis Framework (Formerly Known as QIIME 2 Framework (Q2F))☆528May 18, 2026Updated last week
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆170Sep 4, 2025Updated 8 months ago
- An R package for downstream data analysis of microbiome omics data☆278May 20, 2026Updated last week
- A comprehensive R package for deep mining microbiome☆194Apr 29, 2026Updated last month
- R package for community ecologists: popular ordination methods, ecological null models & diversity analysis☆532Updated this week
- Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.☆285Dec 19, 2022Updated 3 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 biomarker discovery☆198Feb 19, 2025Updated last year
- Interactively explore metagenomes and more from a web browser.☆501Dec 22, 2021Updated 4 years ago
- Sparse InversE Covariance estimation for Ecological Association and Statistical Inference☆231Apr 29, 2026Updated last month
- Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tes…☆92Aug 22, 2025Updated 9 months ago
- MaAsLin2: Microbiome Multivariate Association with Linear Models☆155Feb 5, 2026Updated 3 months ago
- Qiita - A multi-omics databasing effort☆132May 8, 2026Updated 3 weeks ago
- Tools for visualising microbial community amplicon data☆72Nov 3, 2025Updated 6 months ago
- Visualization and annotation of phylogenetic trees☆926Apr 29, 2026Updated last month
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆74Sep 1, 2022Updated 3 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.
- An interactive web application for demonstrating and using phyloseq.☆60Jul 18, 2019Updated 6 years ago
- Miscellaneous functions for metagenomic analysis.☆54May 14, 2026Updated 2 weeks ago
- bioBakery tools for meta'omic profiling☆315Jun 3, 2025Updated 11 months ago
- Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…☆278Jan 13, 2026Updated 4 months ago
- Network construction, analysis, and comparison for microbial compositional data☆179Dec 18, 2025Updated 5 months ago
- Fast genome-wide functional annotation through orthology assignment☆737May 22, 2026Updated last week
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆244May 12, 2026Updated 2 weeks ago
- Versatile open-source tool for microbiome analysis☆748May 4, 2026Updated 3 weeks ago
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆406May 22, 2026Updated last week
- 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.
- Rapid prokaryotic genome annotation☆981Jan 6, 2026Updated 4 months ago
- Ying's tools for analysis, with particular focus on microbiome data☆40May 20, 2026Updated last week
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆599May 20, 2026Updated last week
- FUNGuild: parsing OTUs into functional guilds☆131Apr 26, 2024Updated 2 years ago
- Handy tools for Microbiome analysis in R☆18May 22, 2019Updated 7 years ago
- R implementation of the LEfSe method☆66May 14, 2026Updated 2 weeks ago
- Visualize microbiome data with black magic ggtree☆68Sep 3, 2020Updated 5 years ago