Course: Exploring the Landscape of Antibiotic Resistance in Microbiomes

The name ResistoXplorer is derived from the connection of two words: Resistome and Explorer. This denomination explains the purpose behind it, which is to allow visualisation, statistical and exploratory analysis …

To understand the downstream analysis of data, let’s imagine a story together. Of course, this specific case is fictional, but it could very well be real! “Dr. Patricia just started …

In this video, you will learn how to intuitively explore, manipulate and customize the ARG-microbial host association networks in ResistoXplorer. We recommend you follow along on your own computer and …

Until now, we have learned to visualise and analyse the ARG abundance table and how to find associations between ARGs and taxa’s using various univariate and multivariate statistical techniques. Another …

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The microbiome harbors a collection of antimicrobial resistance genes (ARGs) known as the resistome. Metagenomics-based studies are used to characterize the resistome and the taxonomic composition of microbial communities. The …

In this video, you will learn on how to perform differential abundance testing to identify significant features (ARGs) using various statistical methods implemented in ResistoXplorer.

One of the main aims of the metagenomic-based resistome studies is to identify significant differences in resistance gene abundances between samples. Although it sounds straightforward, several technical challenges remain, most …

Beta diversity characterises differences in the ARG or resistome composition between samples. There are several beta diversity indices/measures that can be used to generate a distance or dissimilarity scores to …

Metagenomic resistome data are multi-dimensional, often represented by hundreds or thousands of different ARGs, and therefore deducing meaningful results is not only dependent on the abundance of single ARGs, but …

One of the most basic and first questions that arise in metagenomics-based resistome studies are what antimicrobial resistance genes (ARGs) are there and in what proportion are they present in …

In this video, we will demonstrate how to perform various types of normalisation on resistome data in ResistoXplorer. When the video is playing, please follow along on your computer!

You have probably learned at some time in your life that completing whole antibiotic courses prevents bacteria from becoming resistant. While this is true for infections with microbes such as …

Now that data is filtered, we need to normalise it. But why do we need to normalise data? Well, metagenomic data have some unique characteristics such as large differences in …

Alright, now we have uploaded data into ResistoXplorer. Can we start generating some nice figures? Not yet! We first need to process the data that was uploaded, and this is …