A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
☆117Apr 11, 2023Updated 2 years ago
Alternatives and similar repositories for Tools-Microbiome-Analysis
Users that are interested in Tools-Microbiome-Analysis are comparing it to the libraries listed below
Sorting:
- An R package for microbial community analysis in an environmental context☆67Sep 23, 2020Updated 5 years ago
- microbiome R package☆311Aug 19, 2025Updated 6 months ago
- A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.☆457Feb 13, 2026Updated 2 weeks ago
- Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing☆125May 12, 2024Updated last year
- Microbiome research☆21May 24, 2022Updated 3 years ago
- A comprehensive R package for deep mining microbiome☆191Nov 3, 2025Updated 3 months ago
- R package for microbiome biomarker discovery☆193Feb 19, 2025Updated last year
- Visualize microbiome data with black magic ggtree☆68Sep 3, 2020Updated 5 years ago
- A comprehensive and customizable R package for microbiome analysis.☆23Aug 10, 2025Updated 6 months ago
- 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
- METAgenomic LONgitudinal Differential Abundance method☆16Dec 17, 2019Updated 6 years ago
- Code, unit tests, and tutorials for running PICRUSt2☆381Nov 27, 2025Updated 3 months ago
- The is mostly a wrapper tool using phyloseq and microbiome R packages.☆32Nov 23, 2022Updated 3 years ago
- Ying's tools for analysis, with particular focus on microbiome data☆41Jan 27, 2026Updated last month
- The Microbiome Interpretable Temporal Rule Engine☆46May 26, 2021Updated 4 years ago
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆73Sep 1, 2022Updated 3 years ago
- R package for annotating metagenomic datasets with taxonomic information☆10Feb 11, 2020Updated 6 years ago
- statdivlab's teaching materials for STAMPS @ the MBL in 2019☆11Jul 28, 2019Updated 6 years ago
- ☆20Jun 8, 2020Updated 5 years ago
- ☆13Feb 5, 2022Updated 4 years ago
- An R package for data analysis in microbial community ecology☆269Updated this week
- Miscellaneous functions for metagenomic analysis.☆53Feb 20, 2026Updated last week
- diversity estimation under ecological networks☆83Jul 29, 2025Updated 7 months ago
- ☆12Apr 6, 2021Updated 4 years ago
- A set of R scripts for the analysis of microbial profiles☆41Jan 9, 2026Updated last month
- Neural networks for microbe-metabolite interaction analysis☆129Nov 4, 2022Updated 3 years ago
- ☆12Oct 28, 2021Updated 4 years ago
- R interface to GenBank/GenPept files☆14Jan 12, 2021Updated 5 years ago
- Curated Metagenomic Data of the Human Microbiome☆150Jan 21, 2026Updated last month
- R package for downstream Microbiome analysis☆31Dec 10, 2024Updated last year
- Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data☆144Feb 6, 2026Updated 3 weeks ago
- SourceTracker2☆86Jul 10, 2024Updated last year
- A complete pipeline for metagenomic analysis☆441Jan 21, 2026Updated last month
- Sparse InversE Covariance estimation for Ecological Association and Statistical Inference☆229Oct 29, 2025Updated 4 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 4 months ago
- mapping files for MetaCyc pathway☆12Sep 14, 2019Updated 6 years ago
- ATLAS - Three commands to start analyzing your metagenome data☆402Nov 28, 2025Updated 3 months ago
- Transform files to the microtable object with microeco package☆28Feb 13, 2026Updated 2 weeks ago
- This is the source code for the "Analysis of Microbiome Community Data in R" ICPP 2018 workshop. The website is available at: https://gr…☆16Nov 30, 2023Updated 2 years ago