Why R? Webinar 029 - Using R for analysis of the human microbiome
- full title: Why using R for analysis of the human microbiome is a good idea
- stream https://youtu.be/tUWvYnGzfJg
- speaker Susan Holmes http://statweb.stanford.edu/~susan/
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High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or composition of bacterial communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2, structSSI and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork and ggraph packages.
Trained in the French school of Data Analysis in Montpellier, Susan Holmes has been working in non parametric multivariate statistics applied to Biology since 1985. She has taught at MIT, Harvard and was an Associate Professor of Biometry at Cornell before moving to Stanford in 1998. She created the Thinking Matters class: Breaking Codes and Finding patterns and likes working on big messy data sets, mostly from the areas of Immunology, Cancer Biology and Microbial Ecology. Her theoretical interests include applied probability, MCMC (Monte Carlo Markov chains), Graph Limit Theory, Differential Geometry and the topology of the space of Phylogenetic Trees. She wrote the book Modern Statistics for Modern Biology with Wolfgang Huber from EMBL and teaches the material as a crash course (BIOS221) regularly every year. Her current focus is improving the statistical analyses and reproducibility of data in perturbation studies of the Human Microbiome.