The importance of converting relative to absolute abundance in the context of microbial ecology: Introducing the user-friendly DspikeIn R package
This repository contains code for pre-processing and analysis of 16S rRNA data used to generate results in the paper "Skin bacterial community dynamics of hands and forearms before and after military field exercise".
The unified functional prediction and comparative analysis for 16S rRNA gene sequencing data
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
q2-boots: bootstrapped and rarefaction-based alpha and beta diversity analyses 🥾
Command line tool that writes commands to run one by one to perform analyses (mainly using qiime2) on a HPC running Slurm, Torque or none of these.
A collection of code used in the analysis and visualization of 16S sequencing data (among other things) @ Michigan State University over the course of my master's degree.
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
Materials and presentation for the 2023 ISB Microbiome course.
Metagenomic analysis of the project: "PROGRAMAÇÃO METABÓLICA INDUZIDA PELA SUPERLACTAÇÃO E SEUS EFEITOS NA ATIVAÇÃO DO INFLAMASSOMA NLRP3 E EXPRESSÃO DO MIR-155 EM MODELO EXPERIMENTAL DE RESISTÊNCIA À INSULINA"
QIIME2 worklflow. From raw data to a feature table.
A fast and scalable phylogenetic tree viewer for microbiome data analysis
16S rRNA sequencing data analysis of mice fed with pectin-based prebiotic fiber using both QIIME2 and R.
Comparative study of soil microbiome using QIIME2
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