Posts

Wrench Normalization for Sparse Microbiome Data

I recently attended a seminar where Wrench normalization was shown to have good performance in the presented simulation studies. So I thought I would give it another look.
Last updated on Jul 15, 2021 22 min read Microbiome

Identifying Differentially Abundant Features in Microbiome Data

A common goal in many microbiome studies is to identify features (i.e., species, OTUs, gene families, etc.) that differ according to some study condition of interest. While often done, this is a difficult task, and in the Introduction to the Statistical Analysis of Microbiome Data in R post I touch on some of the reasons for this.
Last updated on Apr 9, 2021 14 min read Microbiome

Taxonomic and Functional Profiling using Biobakery Workflows

Below I provide scripts to implement the current default workflow for taxonomic and functional profiling using the Huttenhower Lab’s Biobakery Tool Suite used by the Microbial Metagenomics Analysis Center (MMAC) at CCHMC for paired-end data.
Last updated on Apr 9, 2021 11 min read Microbiome

Denoising Amplicon Sequence Variants Using DADA2, DeBlur, and UNOISE3 with QIIME2

Below I provide scripts to implement several workflows for denoising 16s rRNA gene sequences used by the Microbial Metagenomics Analysis Center (MMAC) at CCHMC for paired-end data. These scripts are written to run on the CCHMC high-performance computing (HPC) cluster.
Last updated on Nov 30, 2020 12 min read Microbiome

Profiling of Shotgun Metagenomic Sequence Data using Kraken2/Bracken and HUMAnN2

Below I provide scripts to implement the current default workflow for taxonomic profiling using Kraken2 and Bracken and functional profiling using HUMAnN2 used by the Microbial Metagenomics Analysis Center (MMAC) at CCHMC for paired-end data.
Last updated on Nov 25, 2020 15 min read Microbiome

An Introduction to the Harrell“verse”: Predictive Modeling using the Hmisc and rms Packages

This is post is to introduce members of the Cincinnati Children’s Hospital Medical Center R Users Group (CCHMC-RUG) to some of the functionality provided by Frank Harrell’s Hmisc and rms packages for data description and predictive modeling.
Last updated on Sep 3, 2019 35 min read Predictive Modeling

Denoising Amplicon Sequence Data Using USEARCH and UNOISE3

During the Introduction to Metagenomics Summer Workshop we discussed denoising amplicon sequence variants and worked through Ben Callahan’s DADA2 tutorial. During that session, I mentioned several other approaches and algorithms for denoising or clustering amplicon sequence data including UNOISE3, DeBlur and Mothur.
Last updated on Aug 21, 2019 10 min read Microbiome

Downloading Amplicon Sequence Runs from the NCBI SRA

A collaborator recently asked if I could help pull down a few thousand sequence files from the NCBI Sequence Read Archive (SRA) for a secondary analysis. This is a short post primarily to help me (and hopefully others) remember how to do this once you have a set of SRR IDs of interest.
Last updated on Aug 21, 2019 3 min read Microbiome

Introduction to Phyloseq

This post is from a tutorial demonstrating the processing of amplicon short read data in R taught as part of the Introduction to Metagenomics Summer Workshop. It provides a quick introduction some of the functionality provided by phyloseq and follows some of Paul McMurdie’s excellent tutorials.
Last updated on Jul 28, 2019 18 min read Microbiome

Introduction to the Statistical Analysis of Microbiome Data in R

This post is also from the Introduction to Metagenomics Summer Workshop and provides a quick introduction to some common analytic methods used to analyze microbiome data. I thought it might be of interest to a broader audience so decided to post it here.
Last updated on Jul 28, 2019 53 min read Microbiome