Chordomics: A visualization tool for linking function to phylogeny in microbiomes

Kevin McDonnell; Nicholas Waters; Enda Howley; Florence Abram

doi:10.1093/bioinformatics/btz711

Chordomics: A visualization tool for linking function to phylogeny in microbiomes

Kevin McDonnell
, Nicholas Waters
, Enda Howley
, Florence Abram

Computer Science

Ryan Institute
The James Hutton Institute
University of Galway

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

The overarching aim of microbiome analysis is to uncover the links between microbial phylogeny and function in order to access ecosystem functioning. This can be done using several experimental strategies targeting different biomolecules, including DNA (metagenomics), RNA (metatranscriptomics) and proteins (metaproteomics). Despite the importance of linking microbial function to phylogeny there are currently no visualization tools that effectively integrate this information. Chordomics is a Shiny-based application for linked-omics data analysis, allowing users to visualize microbial function and phylogeny on a single plot and compare datasets across time and environments. Availability and implementation: Chordomics is available on GitHub: https://github.com/kevinmcdonnell6/chordo mics; software is coded in R and JavaScript and a demonstration version is available at https://kmcd.shinyapps.io/ChordomicsDemo/.

Original language	English
Pages (from-to)	1309-1310
Number of pages	2
Journal	Bioinformatics
Volume	36
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/btz711
State	Published - Feb 15 2020

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abstract = "The overarching aim of microbiome analysis is to uncover the links between microbial phylogeny and function in order to access ecosystem functioning. This can be done using several experimental strategies targeting different biomolecules, including DNA (metagenomics), RNA (metatranscriptomics) and proteins (metaproteomics). Despite the importance of linking microbial function to phylogeny there are currently no visualization tools that effectively integrate this information. Chordomics is a Shiny-based application for linked-omics data analysis, allowing users to visualize microbial function and phylogeny on a single plot and compare datasets across time and environments. Availability and implementation: Chordomics is available on GitHub: https://github.com/kevinmcdonnell6/chordo mics; software is coded in R and JavaScript and a demonstration version is available at https://kmcd.shinyapps.io/ChordomicsDemo/.",

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Chordomics: A visualization tool for linking function to phylogeny in microbiomes

Abstract

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