R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
☆24Jan 24, 2024Updated 2 years ago
Alternatives and similar repositories for mbtools
Users that are interested in mbtools are comparing it to the libraries listed below
Sorting:
- ☆22Nov 6, 2020Updated 5 years ago
- METAgenomic LONgitudinal Differential Abundance method☆16Dec 17, 2019Updated 6 years ago
- Count Regression for Correlated Observations with the Beta-binomial☆106Nov 13, 2025Updated 3 months ago
- Python package to study microbial communities using metabolic modeling.☆120Jan 26, 2026Updated last month
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated last year
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆19Updated this week
- Pipelines used in the lab.☆15Mar 26, 2025Updated 11 months ago
- Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations☆14Nov 24, 2025Updated 3 months ago
- SPecies level IdentificatioN of metaGenOmic amplicons☆11Apr 11, 2018Updated 7 years ago
- ☆43Jul 31, 2017Updated 8 years ago
- Database of genomes integrated from the gut microbiome and other environments☆45Feb 3, 2023Updated 3 years ago
- Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check …☆31Oct 19, 2020Updated 5 years ago
- Functions for compositional analysis of high throughput sequencing☆29Dec 8, 2023Updated 2 years ago
- R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.☆122Feb 17, 2026Updated last week
- Vanilla regression methods for microbiome differential abundance analysis☆61Nov 3, 2020Updated 5 years ago
- ** Blood metabolome predicts gut microbiome α-diversity in humans**☆24Sep 23, 2019Updated 6 years ago
- Maximum Likelihood Amplicon Pipeline☆22May 22, 2024Updated last year
- tidyMicro GitHup Repository☆21Nov 17, 2021Updated 4 years ago
- Snakemake workflow to map and quantify microbial genomes in metagenomic reads☆13Oct 10, 2025Updated 4 months ago
- ☆11Apr 5, 2021Updated 4 years ago
- R package for downstream Microbiome analysis☆31Dec 10, 2024Updated last year
- A comprehensive and customizable R package for microbiome analysis.☆23Aug 10, 2025Updated 6 months ago
- Code used in MiCE 8992 Spring 2016☆44Apr 19, 2016Updated 9 years ago
- Metabolic scanning and annotation of Metagenomes☆10Dec 18, 2025Updated 2 months ago
- Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut☆10Jun 25, 2024Updated last year
- ☆10Sep 26, 2019Updated 6 years ago
- statdivlab's teaching materials for STAMPS @ the MBL in 2019☆11Jul 28, 2019Updated 6 years ago
- ☆17May 21, 2025Updated 9 months ago
- ☆20Jun 8, 2020Updated 5 years ago
- Species richness with high diversity☆68Aug 5, 2025Updated 6 months ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆67Updated this week
- R package for Statistical Inference of Associations between Microbial Communities And host phenoType☆58Jan 30, 2024Updated 2 years ago
- Assessing the quality of prokaryotic genomes, filtering and dereplication☆11Aug 26, 2022Updated 3 years ago
- An R package for data analysis in microbial community ecology☆269Updated this week
- microbiome R package☆311Aug 19, 2025Updated 6 months ago
- A package for creating and managing sample identifiers in comparative -omics datasets.☆23Jan 30, 2017Updated 9 years ago
- diversity estimation under ecological networks☆83Jul 29, 2025Updated 7 months ago
- ☆12Oct 3, 2023Updated 2 years ago
- An automated pipe for reproducible RNA-seq analysis with the minimal efforts from researchers. You only need to provide the taxa name and…☆14Mar 4, 2022Updated 3 years ago