Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data
Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data - Published in JOSS (2021)
MicrobiomeR
MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows - Published in JOSS (2019)
pymgpipe
pymgpipe: microbiome metabolic modeling in Python - Published in JOSS (2023)
Sourcepredict
Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification - Published in JOSS (2019)
MiNAA
MiNAA: Microbiome Network Alignment Algorithm - Published in JOSS (2024)
microViz
microViz: an R package for microbiome data visualization and statistics - Published in JOSS (2021)
ANCOMBC
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
metagem
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://github.com/biocore/qurro
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
sccomp
Mixed-effect model to test differences in cell type proportions from single-cell data, in R
https://github.com/cafferychen777/ggpicrust2
Make Picrust2 Output Analysis and Visualization Easier
singlem
Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
https://github.com/biocore/gemelli
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
emperor
Emperor a tool for the analysis and visualization of large microbial ecology datasets
https://github.com/biocore/birdman
Bayesian Inferential Regression for Differential Microbiome Analysis
https://github.com/biocore/empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis
dada2
Accurate sample inference from amplicon data with single nucleotide resolution
https://github.com/erictleung/shinydiversity
Interactive application to explore various ecological diversity metrics
https://github.com/erictleung/microbiome-analysis-resources
:microscope: Resources and notes on studying the human microbiome
https://github.com/biocore/qadabra
Snakemake workflow for comparison of differential abundance ranks
https://github.com/biocore/calour
exploratory and interactive microbiome analyses based on heatmaps
multimedia
multimedia is an R package for multimodal mediation analysis of microbiome data. It has been designed to help integration of relative abundance, survey, and metabolomic data through causal mediation analysis.
decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
https://github.com/biocore/qiime
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
https://github.com/erictleung/phyloseq-cheatsheet
:notebook: Minimal cheatsheet for functions in the phyloseq R package
https://github.com/bioatmosphere/microbiome-drought-legacy
A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.
https://github.com/erictleung/microbetv-papers
:headphones: Papers discussed on various shows on MicrobeTV
https://github.com/dalmolingroup/mare-methods
MaRe (Metagenômica de Mangue e Restinga)
veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
parafac4microbiome
Creation and selection of Parallel Factor Analysis models of longitudinal microbiome data.
2022-12-08-shotgun-metagenomics-workshop
Data Carpentry workshop organised at Utrecht University Medical Center on December 8-9, 2022.
https://github.com/bigdatabiology/videotutorials
Supporting material for YouTube tutorials
machine-learning-toolbox
Interactive table for "Marcos Zambrano et al. (2023) A Toolbox of Machine Learning Software to Support Microbiome Analysis. Frontiers in Microbiology 14, 1250806"
https://github.com/biocore/q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
eggsurfacemicrobiome
Reproducible documentation for "Heussler and Klammsteiner et al. (2023). Microbial influences on black soldier fly reproduction: A focus on egg surface colonization. Research Square Preprint"
https://github.com/cafferychen777/microbiomestat-shiny
A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.
detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
atavide_lite
A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings are specific for our compute resources
https://github.com/cafferychen777/microbiomestat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
https://github.com/cafferychen777/microbiomestat-turtorial-professional-version
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
https://github.com/cafferychen777/microbiomedaacomp
A comprehensive R toolkit for comparing and evaluating Differential Abundance Analysis (DAA) methods in microbiome studies.
https://github.com/erictleung/dada2hpcpipe
:ocean: 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM
https://github.com/ahmedmoustafa/als
Analysis of the gut microbiome of Amyotrophic Lateral Sclerosis (ALS) patients using the DADA2 workflow