The R Journal: article published in 2016, volume 8:2

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages PDF download
Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Zinovyev and Eric Bonnet , The R Journal (2016) 8:2, pages 293-306.

Abstract Biological pathways or modules represent sets of interactions or functional relationships occurring at the molecular level in living cells. A large body of knowledge on pathways is organized in public databases such as the KEGG, Reactome, or in more specialized repositories, the Atlas of Cancer Signaling Network (ACSN) being an example. All these open biological databases facilitate analyses, improving our understanding of cellular systems. We hereby describe ACSNMineR for calculation of enrichment or depletion of lists of genes of interest in biological pathways. ACSNMineR integrates ACSN molecular pathways gene sets, but can use any gene set encoded as a GMT file, for instance sets of genes available in the Molecular Signatures Database (MSigDB). We also present RNaviCell, that can be used in conjunction with ACSNMineR to visualize different data types on web-based, interactive ACSN maps. We illustrate the functionalities of the two packages with biological data taken from large-scale cancer datasets.

Received: 2016-04-02; online 2016-10-21
CRAN packages: ACSNMineR, RNaviCell, ggplot2 , CRAN Task Views implied by cited CRAN packages: Graphics, Phylogenetics , Bioconductor packages: GOstats, clusterProfiler


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@article{RJ-2016-047,
  author = {Paul Deveau and Emmanuel Barillot and Valentina Boeva and
          Andrei Zinovyev and Eric Bonnet},
  title = {{Calculating Biological Module Enrichment or Depletion
          and Visualizing Data on Large-scale Molecular Maps with
          ACSNMineR and RNaviCell Packages}},
  year = {2016},
  journal = {{The R Journal}},
  url = {https://journal.r-project.org/archive/2016/RJ-2016-047/index.html},
  pages = {293--306},
  volume = {8},
  number = {2}
}