Make Picrust2 Output Analysis and Visualization Easier
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Python package to study microbial communities using metabolic modeling.
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
Open-source opinionated Galaxy-based framework for microbiota analysis
Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output
📓 Minimal cheatsheet for functions in the phyloseq R package
Data and analysis code for the Indian gut microbiota study
Improved bee microbiota characterization using routine 16S rRNA gene sequencing 🐝🧬
Comprehensive KEGG Data Retrieval Using Multiple Sources
Meta-analysis on human gut microbiota in Colorectal cancer
Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.
biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.
Code for reproducing results in the paper: "Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon"
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
Les études de métagénomiques mettent en évidence la présence et l'absence de différentes souches dans un microbiome. Pour résumer les abondances, on peut établir des graphes de co-occurence via : Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data, Janko Tackmann, Joao Frederico ...
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