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microbiome-analysis

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microbiome /microbiome

microbiome R package

r microbiology microbiome microbiome-analysis phyloseq human-microbiome population-study hitchip hitchip-atlas

UpdatedAug 19, 2025
R

opencobra /cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

tutorial metabolomics reconstruction transcriptomics cobra metabolic-models strain-engineering metabolic-reconstruction constraint-based-modeling microbiome-analysis metabolic-engineering gap-filling cobra-toolbox omics-data-integration human-metabolism

UpdatedDec 10, 2025
MATLAB

YuLab-SMU /MicrobiotaProcess

🦠 A comprehensive R package for deep mining microbiome

rstats microbiome microbiome-analysis microbiome-data

UpdatedNov 3, 2025
R

qiita-spots /qiita

Qiita - A multi-omics databasing effort

python microbiome microbiome-analysis

UpdatedDec 16, 2025
Python

david-barnett /microViz

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

r rstats microbiome microbiota microbiome-analysis

UpdatedAug 1, 2025
R

grimmlab /MicrobiomeBestPracticeReview

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

bioinformatics pipeline best-practices assembly metagenomics microbiome biomedical microbiome-analysis amplicon-sequencing 16s-rrna microbiome-workflow

UpdatedMay 12, 2024
Shell

microsud /Tools-Microbiome-Analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

metagenomics microbial-communities amplicon microbiota microbiome-analysis amplicon-sequencing microbiome-data 16s-rrna

UpdatedApr 11, 2023
CSS

zoecastillo /microbiomeExplorer

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.

microbiome microbiome-analysis

UpdatedSep 1, 2022
R

Russel88 /MicEco

Various functions for analysis of microbial community data

microbial-communities microbiome 16s microbiome-analysis microbial-ecology amplicon-sequencing null-model

UpdatedOct 1, 2025
R

cafferychen777 /MicrobiomeStat

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

visualization statistics longitudinal-data microbiome omics metagenomes metagenomic-analysis microbiome-analysis phyloseq dada2 omics-data-integration amplicon-sequencing microbiome-data qiime2 16s-rrna microbiome-workflow

UpdatedNov 23, 2025
R

microsud /microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.

sequencing metagenomics microbial-communities microbiome amplicon 16s microbiome-analysis core-microbiome qc-pipeline

UpdatedNov 23, 2022
R

waldronlab /curatedMetagenomicDataAnalyses

Analyses in R and Python Using curatedMetagenomicData

r bioconductor microbiome-analysis microbiome-data r01ca230551

UpdatedNov 16, 2025
Python

GPZ-Bioinfo /tmap

topological data analysis of population-scale microbiomes

topological-data-analysis microbiome-analysis

UpdatedJan 27, 2023
Python

wijerasa /bioinformatics-projects

A Collection of Bioinformatics Projects

python r 16s microbiome-analysis

UpdatedSep 19, 2018
Python

vallenderlab /MicrobiomeR

A comprehensive and customizable R package for microbiome analysis.

visualization bioinformatics r color-palette metagenomics rstats beta-diversity microbial-genomics microbiology microbiome pcoa microbiome-analysis phyloseq comprehensive permanova alpha-diversity metacoder

UpdatedAug 10, 2025
R

mikemc /metacal

Metagenomics calibration R package

metagenomics r-package microbiome-analysis marker-gene-analysis amplicon-sequencing

UpdatedFeb 15, 2022
R

CMU-SAFARI /Genome-on-Diet

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

bioinformatics genomics metagenomics variant-calling containment-search genome-analysis large-scale sequence-alignment read-mapping metagenomic-analysis microbiome-analysis minimap2 wavefront-alignment genome-on-diet

UpdatedSep 4, 2024
Roff

statdivlab /paramedic

Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations

bayesian-methods statistical-inference stan microbiome-analysis

UpdatedNov 24, 2025
R

smdabdoub /phylotoast

Tools for phylogenetic data analysis including visualization and cluster-computing support.

visualization python bioinformatics cross-platform hpc slurm computational-biology phylogenetics microbial-genomics microbiome 16s qiime pbs microbiome-analysis

UpdatedDec 18, 2021
Python

guokai8 /microbial

Do microbiome analysis with dada2 and phyloseq object

microbiome microbiome-analysis

UpdatedOct 9, 2024
R

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