An introduction to benchdamic

Workshop description

This workshop provides an introductory example on how to work with the analysis framework firstly proposed in “Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data” by Calgaro et al. (2020) and then formalised in the benchdamic Bioconductor package Calgaro et al. (2023).

We will test a couple of methods for differential abundance (DA) analysis on a microbiome dataset and we will see how to test custom methods on the same dataset. Performances of each method are evaluated with respect to i) suitability of distributional assumptions (GOF), ii) ability to control false positives (TIEC), iii) concordance of the findings, and iv) enrichment of DA microbial species in specific conditions.

Pre-requisites

  • Intermediate knowledge of R syntax
  • Familiarity with the phyloseq or TreeSummarizedExperiment classes
  • Familiarity with DA analysis in microbiome data

Some suggested background readings for the workshop:

  • “Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data” by Calgaro et al. (2020)
  • “Microbiome differential abundance methods produce different results across 38 datasets” by Nearing et al. (2022);
  • “Normalization and microbial differential abundance strategies depend upon data characteristics” by Weiss et al. (2017);
  • “benchdamic: benchmarking of differential abundance methods for microbiome data” by Calgaro et al. (2023).

Preparation

To be able to follow along with this workshop, we have created a Docker installation. In order to access this, you need to first install Docker on your own computer. Once you have done that, you can then load the Docker container for this workshop by starting Docker and writing the following line in your terminal:

docker run -e PASSWORD=<choose_a_password_for_rstudio> -p 8787:8787 ghcr.io/mcalgaro93/benchdamicworkshop

You can choose any password for rstudio - that’s what you will use to log in. It will take some time for the Docker to be downloaded and started, so you might consider doing this ahead of time.

In linux, you may experience an error: “docker: Got permission denied while trying to connect to the Docker daemon socket…”. To solve it just run the command with sudo privilegies or follow this thread.

Once running, navigate to http://localhost:8787/ and then login with ‘rstudio’ as username and the chosen password as password.

Then please open the file ‘vignettes/introduction_to_benchdamic.Rmd’ to start the workshop.

You can also see the workshop material at https://mcalgaro93.github.io/benchdamicWorkshop/.