Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
sra
 
 
 
 
 
 
 
 

Data and analysis for Thanissery et al (2019)

DOI

This repository contains the microbiome data analysis for the manuscript

Thanissery R, McLaren MR, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston JA, Jacob M, Callahan BJ, Theriot CM. 2019. Characterization of C. difficile strains isolated from companion animals and the associated changes in the host fecal microbiota. bioRxiv 822577. doi:10.1101/822577

The raw sequence reads are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562547. The results of bioinformatic analysis of the raw reads with DADA2, including taxonomy assignment against Silva v132 using DADA2's assignTaxonomy() and addSpecies() functions are in results/dada2, and as a phyloseq object in results/ps.Rds.

The results/ folder also includes plain-text (.csv format) tables mapping ASV names to their amplicon sequence and taxonomy. These tables can be viewed directly in a web browser by clicking the below links.

All bioinformatic and statistical analyses are contained in R-markdown documents in analysis/. A description of these files and links to rendered versions showing all numerical output and figures is given in analysis/README.md.

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Packages

No packages published

Languages