Applications of Community Detection Algorithms to Large Biological Datasets

Methods Mol Biol. 2021:2243:59-80. doi: 10.1007/978-1-0716-1103-6_3.


Recent advances in data acquiring technologies in biology have led to major challenges in mining relevant information from large datasets. For example, single-cell RNA sequencing technologies are producing expression and sequence information from tens of thousands of cells in every single experiment. A common task in analyzing biological data is to cluster samples or features (e.g., genes) into groups sharing common characteristics. This is an NP-hard problem for which numerous heuristic algorithms have been developed. However, in many cases, the clusters created by these algorithms do not reflect biological reality. To overcome this, a Networks Based Clustering (NBC) approach was recently proposed, by which the samples or genes in the dataset are first mapped to a network and then community detection (CD) algorithms are used to identify clusters of nodes.Here, we created an open and flexible python-based toolkit for NBC that enables easy and accessible network construction and community detection. We then tested the applicability of NBC for identifying clusters of cells or genes from previously published large-scale single-cell and bulk RNA-seq datasets.We show that NBC can be used to accurately and efficiently analyze large-scale datasets of RNA sequencing experiments.

Keywords: Big data; Community detection; Networks based clustering; Single-cell RNA sequencing.

MeSH terms

  • Algorithms*
  • Cluster Analysis*
  • Data Analysis*
  • Datasets as Topic
  • Gene Expression Profiling / methods
  • Humans
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis / methods