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The Top 23 R Microbiome Open Source Projects

Open source projects categorized as R Microbiome
Dada2 ⭐ 428
Accurate sample inference from amplicon data with single nucleotide resolution
most recent commit 3 months ago
Microbiome ⭐ 257
microbiome R package
most recent commit 9 months ago
Microbiomemarker ⭐ 151
R package for microbiome biomarker discovery
most recent commit 6 months ago
Microbiotaprocess ⭐ 150
🦠 A comprehensive R package for deep mining microbiome
most recent commit 4 months ago
Decontam ⭐ 122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
most recent commit a year ago
Ancombc ⭐ 87
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
most recent commit 4 months ago
Maaslin2 ⭐ 86
MaAsLin2: Microbiome Multivariate Association with Linear Models
most recent commit 7 months ago
Microviz ⭐ 80
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
most recent commit 3 months ago
Oma ⭐ 69
Orchestrating Microbiome Analysis
most recent commit 3 months ago
Ggpicrust2 ⭐ 59
Make Picrust2 Output Analysis and Visualization Easier
total releases 10most recent commit 3 months ago
Ancom Code Archive ⭐ 47
R functions for Analysis of Composition of Microbiomes (ANCOM).
most recent commit 2 years ago
Microbiomeexplorer ⭐ 44
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.
most recent commit 2 years ago
Mia ⭐ 42
Microbiome analysis
most recent commit 5 months ago
Sccomp ⭐ 37
Robust differential composition and variability analysis for single-cell data
most recent commit 3 months ago
Microbiomeviz ⭐ 36
Visualize microbiome data with black magic ggtree
most recent commit 4 years ago
Datest ⭐ 34
Compare different differential abundance and expression methods
most recent commit 2 years ago
Microbiomeutilities ⭐ 29
The is mostly a wrapper tool using phyloseq and microbiome R packages.
most recent commit a year ago
Miceco ⭐ 28
Various functions for analysis of microbial community data
most recent commit a year ago
Schtools ⭐ 26
Schloss Lab Tools for Reproducible Microbiome Research 💩
most recent commit 8 months ago
Melonnpan ⭐ 24
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
most recent commit a year ago
Tweedieverse ⭐ 24
Differential analysis of multi-omics data based on the Tweedie distribution
most recent commit 5 months ago
Microbiomestat ⭐ 18
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
most recent commit 3 months ago
Microbiomer ⭐ 17
A comprehensive R package for microbiome analysis.
most recent commit a year ago
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