The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
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Updated
May 27, 2024 - MATLAB
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Qiita - A multi-omics databasing effort
microbiome R package
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
🦠 A comprehensive R package for deep mining microbiome
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.
Various functions for analysis of microbial community data
accessory functions for processing microbial community data
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
topological data analysis of population-scale microbiomes
Microbiome Analysis Plotting and Visualization
Mothur procedures for 16S and ITS analysis
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Building the software for analyzing the microbiome data using machine learning technics. the application provides the GUI for the user they can easily analyze the data without any other programming knowledge developed by @piriyaraj @varnaraj @thanujan @Rilwan292
Analyses in R and Python Using curatedMetagenomicData
A Collection of Bioinformatics Projects
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
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).
Tools for phylogenetic data analysis including visualization and cluster-computing support.
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