Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials

Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms (microbes) obtained from a common habitat. Metagenomics and other “omics” disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. There are plenty of studies using metagenomics which examine microorganisms that inhabit niches in the human body, sometimes causing disease, and are often correlated with multiple treatment conditions. No matter from which environment it comes, the analyses are often aimed at determining either the presence or absence of specific species of interest in a given metagenome or comparing the biological diversity and the functional activity of a wider range of microorganisms within their communities. The importance increases for comparison within different environments such as multiple patients with different conditions, multiple drugs, and multiple time points of same treatment or same patient. Thus, no matter how many hypotheses we have, we need a good understanding of genomics, bioinformatics, and statistics to work together to analyze and interpret these datasets in a meaningful way. This chapter provides an overview of different data analyses and statistical approaches (with example scenarios) to analyze metagenomics samples from different medical projects or clinical trials

Cluster Sculptor, an interactive visual clustering system

International audienceThis paper describes Cluster Sculptor, a novel interactive clustering system that allows a user to iteratively update the cluster labels of a data set, and an as-sociated low-dimensional projection. The system is fed by clustering results computed in a high-dimensional space, and uses a 2D projection, both as sup-port for overlaying the cluster labels, and engaging user interaction. By easily interacting with elements directly in the visualization, the user can inject his or her domain knowledge progressively, crafting an updated 2D projection and the associated clustering structure that combine his or her preferences and the manifolds underlying the data. Via interactive controls, the distribution of the data in the 2D space can be used to amend the cluster labels, or reciprocally, the 2D projection can be updated so as to emphasize the current clusters. The 2D projection updates follow a smooth physical metaphor, that gives insight of the process to the user. Updates can be interrupted any time, for further data inspection, or modifying the input preferences. The interest of the system is demonstrated by detailed experimental scenarios on three real data sets