Introduction Data analysis performed on high-throughput experiments usually produces lists of significantly perturbed genes (RNASeq) or other entities that can be mapped to genes, like genetic variants (whole genome sequencing) or Transcription factor binding sites (chIPSeq). The long lists of genes (often in the order of hundreds or thousands) produced as the outcome of…
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Choice reviews target those seeking critical evaluations of books and electronic resources. Our primary audiences are librarians and teaching faculty who select materials for academic libraries, especially at the undergraduate level, but we also review with an eye toward students—particularly undergraduates—looking for research materials or to supplement work in the classroom.
Networks often contain regions of tightly connected nodes, or clusters, that highlight their shared relationships. An effective way to create a visual summary of a network is to identify clusters and annotate them with an enclosing shape and a summarizing label. Cytoscape provides the ability to annotate a network with shapes and labels, however these annotations must be created manually one at a time, which can be a laborious process. AutoAnnotate is a Cytoscape 3 App that automates the process of identifying clusters and visually annotating them. It greatly reduces the time and effort required to fully annotate clusters in a network, and provides freedom to experiment with different strategies for identifying and labelling clusters. Many customization options are available that enable the user to refine the generated annotations as required. Annotated clusters may be collapsed into single nodes using the Cytoscape groups feature, which helps simplify a network by making its overall structure...