Public data and open source tools for multi-assay genomic investigation of disease

Lavanya Kannan, Marcel Ramos, Angela Re, Nehme El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez Cabrero Lopez, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe-Kains, Levi Waldron*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Citations (Scopus)
225 Downloads (Pure)


Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.

Original languageEnglish
Article numberbbv080
Pages (from-to)603-615
Number of pages13
Issue number4
Early online date10 Oct 2015
Publication statusPublished - 1 Jul 2016


  • Bioconductor
  • Cancer
  • Integrative genomics
  • Multiple assays (multi-assays)
  • Omics
  • Pharmacogenomics
  • Public data


Dive into the research topics of 'Public data and open source tools for multi-assay genomic investigation of disease'. Together they form a unique fingerprint.

Cite this