microbiome R package
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
🦠 A comprehensive R package for deep mining microbiome
Qiita - A multi-omics databasing effort
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
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.
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Various functions for analysis of microbial community data
Analyses in R and Python Using curatedMetagenomicData
topological data analysis of population-scale microbiomes
A Collection of Bioinformatics Projects
The is mostly a wrapper tool using phyloseq and microbiome R packages.
A comprehensive and customizable R package for microbiome analysis.
Metagenomics calibration R package
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).
Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Do microbiome analysis with dada2 and phyloseq object
To associate your repository with the microbiome-analysis topic, visit your repo's landing page and select "manage topics."