GeneAnswers - A collection of bioconductor methods to visualize gene-list annotations

GeneAnswers, integrates GO, DO, KEGG, and caBIO(NCI, Reactome and Biocarta) as well as gene interaction and entrez keywords search for gene set enrichment analysis. Finally, it can automatically generate a html report for one or multiple groups of gene set enrichment analysis with interactive networks.

http://www.bioconductor.org/packages/2.5/bioc/html/GeneAnswers.html

http://www.biomedcentral.com/1756-0500/3/10/abstract

SPIA, a package that seems to provide sophisticated analysis of pathways (including both, gene set enrichment analysis and pathway perturbation analysis)

http://bioinformatics.oxfordjournals.org/content/25/1/75.abstract

http://www.bioconductor.org/packages/devel/bioc/html/SPIA.html