Statistical and Computational methods for Microbiome Studies.

R scripts used for analysis of data reported in Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls

Analysis of amplicon sequencing data with synthetic spike-in standards

Interactive application to explore various ecological diversity metrics

🌊 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM

This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequen…

Analysis for McLaren, Willis, and Callahan (2019)

📢🎯 Generic typing tool from amplicons and/or in silico PCR

microhaplotype visualizer and analyzer

Study of cyanobacterial harmful algal blooms in Lake Erie using autonomous sampling and DNA sequencing

a set of tools for viral amplicon schemes

AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing

A web app for environmental DNA metabarcoding analysis

Metagenomics calibration R package

Utilities for analysis of multiplex amplicon sequencing data

READY TO USE. Repository containing guidelines and templates for archiving amplicon sequencing data with ESS-DIVE repository.

Analysis of skin microbiome of Rana luteiventris frogs from northern Idaho and eastern Washington using QIIME 2, LEfSe, and R.

Various functions for analysis of microbial community data

Building a pipeline for automated 16S analysis from paired short-reads or long-reads