Below is a collection of useful external resources for data processing and analysis in microbial ecology.
Modern Statistics for Modern Biology An easy to digest statistics textbook with a focus on high-throughput sequencing data, written by Prof. Susan Holmes and Dr. Wolfgang Huber.
Bioconductor workflow for microbiome data analysis: from raw reads to community analyses F1000 publication (Callahan et al. 2016) of the bioconductor pipeline for microbiome data analysis. The paper includes R scripts which are clearly annotated.
GUSTA ME: Guide to statistical analysis in microbial ecology A live resource which acts as an excellent primer for common analyses in microbial ecology, with particularly clear and concise explanations of different ordination techinques.
R for Data Science A key text for R in data science, authored by Garrett Grolemund and Hadley Wickham. This text is free to read online, and covers essentials for using R for data analysis.
Best Practives in Dataviz: An R Perspective Interesting commentary on how the choice of visualisation method can influence the interpretation of data. Worth reading when deciding how best to represent your findings.
Coding Club A community based at Edinburgh University focussed on peer-learning statistical skills in R. The site is worth reading regularly, and is an great resource when approaching new challenges with R and its common packages.
R Consortium The R consortium YouTube channel is full of insightful videos from R package developers, including talks from useR conferences. These act as a good resource from broadening your knowledge of R.