On Thursday, January 14th at 7 pm UTC, as part of the Why R? Webinar series, we have the honour to host Susan Holmes from Stanford University. She will talk about microbiomes and how to use R’s workflow to perform sophisticated downstream statistical analysis on those complex bacterial communities.
Looking for more R news? Subscribe to our newsletter and stay updated on our events, and the most relevant news about our beloved open source programming language.
Finally, if you enjoy our content and would like support, donate to the WhyR foundation. We are a volunteer-run non-profit organisation and appreciate your contribution to continue to fulfil our mission.
- 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
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
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.