NetPathMiner: R/Bioconductor package for network path mining through gene expression

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

RCytoscape: tools for exploratory network analysis

(2013) Paul T Shannon et al.   BMC BIOINFORMATICS

rBiopaxParser—an R package to parse, modify and visualize BioPAX data

(2012) Frank Kramer et al.   BIOINFORMATICS

Identifying Neighborhoods of Coordinated Gene Expression and Metabolite Profiles

(2012) Timothy Hancock et al.   PLoS One

Mining metabolic pathways through gene expression

(2010) Timothy Hancock et al.   BIOINFORMATICS

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

(2010) Martijn P van Iersel et al.   BMC BIOINFORMATICS

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY