Repository containing lists of all published ancient metagenomic (and related) samples and libraries
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Updated
Jul 30, 2024 - HTML
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.
Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)
Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
Data, scripts, and outputs for the npj Biofilms and Microbiomes paper "Analysis of microbial compositions: A review of normalization and differential abundance analysis"
R package for calculating specificity in ecological data
Data set for analyzing how a gut microbiome is affected by drinking kombucha
Jekyll Template - Mediumish
How to analyze shotgun metagenomic data with phyloseq - a walkthrough
The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.
Collection of walkthrough tutorials on how to use Tweedieverse for differential analysis of omics data.
Microbiome Study of Lupus Patients
Gut microbiome study (from 2000 to 2020)
Benbow Lab at Michigan State University, Tutorials/example data for analysis of: 16S data, VCF files
Archive: Data, scripts, and outputs for the paper "Sparse Estimation of Correlations among Microbiomes (SECOM)". Please check our ANCOMBC R package for the most up-to-date SECOM functions.
My personal research website
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