R for data science: a book

A Wes Anderson color palette for R

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file form…

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. …

A repository of my Coursera latex code and notes

microbiome R package

🎯 ChIP peak Annotation, Comparison and Visualization

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

🦠 A comprehensive R package for deep mining microbiome

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

diversity estimation under ecological networks

Tools for visualising microbial community amplicon data

Species richness with high diversity

R implementation of MULTI-seq sample classification workflow

Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM function.

R shiny app for interactive microbiome analysis

Project Website:

Microbiome analysis

Speedy versions of phyloseq functions

Comprehensive benchmark of structural variant callers

Ying's tools for analysis, with particular focus on microbiome data

A standalone interactive application for detecting biological significance on a set of genes

Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul

Handy genetics-related R scripts

Adapters for trimming

Code to run the shiny functions for the MASAME suite

Computes affinity between two entities based on their co-occurrence

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

A workshop on microbiome analysis using Bioconductor