Nidelva river through Trondheim Norway

Nidelva river through Trondheim Norway
by Saaru Lindestokke                

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Paul McMurdie

I am currently a Staff Scientist in Biostatistics at Whole Biome, Inc. My research interests revolve around computational biology, with emphasis on open-source tools and the R language in particular.

My publications on Google Scholar

I am currently the lead developer of an R/Bioconductor package for data management and analysis of high-throughput DNA-sequencing based microbiome census data. The package is called phyloseq, and it is developed openly on GitHub, with official development and stable releases of phyloseq available from Bioconductor. I also created a Shiny-based GUI for phyloseq, called shiny-phyloseq, providing support for rapid browser-based data exploration.

I am also an outside contributor to the biom-format project, a general-use format and API for representing biological contingency tables and associated metadata/covariates. I am the lead developer of the R API for the project, which has been released as the biomformat package for R, with an earlier version (now deprecated) on CRAN repository. The Bioconductor version supports both JSON and HDF5 format definitions of biom-format. The latest contributions and development details are available at the biomformat repo on GitHub.

My background is in chemical engineering, environmental engineering, bioinformatics, and most recently, statistics and R development.