qiime2

Amplicon sequencing analysis workflow using DADA2 and QIIME2

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.

A fast and scalable phylogenetic tree viewer for microbiome data analysis

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

A Python package for microbiome sequencing analysis with QIIME 2

Materials and presentation for the 2022 ISB Microbiome course.

Materials and presentation for the 2023 ISB Microbiome course.

Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2

The importance of converting relative to absolute abundance in the context of microbial ecology: Introducing the user-friendly DspikeIn R package

2024"猛犸杯"参赛作品 · 宏基因组学端到端分析流程

A Qiime plugin for MICOM.

QIIME2 worklflow. From raw data to a feature table.

End-to-end metagenomics pipeline for 16S rRNA sequencing data, ecological Alpha/Beta diversity calculations (QIIME2/phyloseq), 3D PCoA projections, and dysbiosis profiling.

Qiime2 Artifact eXtractor

Qiime2 and DADA2 are one of the latest bioinformatics tools used in 16S RNA analysis. The current Qiime2 and DADA2 pipelines support End to End 16S RNA analysis, among other analyses.

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

Effect size calculations for microbiome data

End-to-end 16S microbiome analysis (FASTQ to PCoA) of Crohn's Disease. Implements a QIIME 2 & Docker pipeline to identify significant phylogenetic dysbiosis (p=0.0007).

Microbiome analysis with QIIME2

This is a QIIME2 plugin that annotates sequence data with antimicrobial resistance gene information from CARD.