On Thursday, January 14th at 7 pm UTC, as part of the Why R? Webinar series, we had the honour to host Susan Holmes from Stanford University. She did talk about microbiomes and how to use R’s workflow to perform sophisticated downstream statistical analysis on those complex bacterial communities.
Join us!
Webinar
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Talk
Speaker
- Susan Holmes Author of “Modern Statistics for Biology”, Susan is a Professor of Statistics and member of BioX, Stanford University. She uses computational statistics to draw inferences about many complex biological phenomena, interactions between the immune system and cancer, resilience and biomarker detection in the human microbiome and drug resistance in HIV. She enjoys teaching using R and BioConductor and tries to make everything she does freely available.
Why using R for analysis of the human microbiome is a good idea
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 microbiomes 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.
Sponsor
This event is part of a series sponsored by Jumping Rivers. For more information, check out the JR and WhyR partnership announcement.
Jumping Rivers is an advanced analytics company whose passion is data and machine learning. Our mission is to help clients move from data storage to intelligent data insights leveraging training and setup for data operations with world-leading experts in R and Python.
We offer courses in analytics, data visualisation and programming languages. From individuals to teams, we have what is needed to upscale your skills.
Our courses go from introduction to R and Python to advanced statistical models.
Check out the course’s calendar for 2021.
Questions? Contact us directly.