Bioconductor Software for Graphs
We describe software tools for creating, manipulating, and visualizing graphs in the Bioconductor project. We give the rationale for our design decisions and provide brief outlines of how to make use of these tools. The discussion mirrors that of Chapter 20 where the different mathematical constructs were described. It is worth differentiating between packages that are mainly infrastructure (sets of tools that can be used to create other pieces of software) and packages that are designed to provide an end-user application. The packages graph, RBGL, and Rgraphviz are infrastructure packages. Software developers may use these packages to construct tools aimed at specific applications areas, such as the GOstats package.
KeywordsShort Path Random Graph Minimal Span Tree Edge Weight Short Path Algorithm
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