MicNet toolbox: Visualizing and unraveling a microbial network.

ABSTRACT: Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural

SUBMITTER: Favila N 

PROVIDER: S-EPMC9231805 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature