Kannan, LavanyaRamos, MarcelRe, AngelaEl-Hachem, NehmeSafikhani, ZhalehGendoo, Deena M. A.Davis, SeanGomez Cabrero, DavidCastelo Valdueza, RobertHansen, Kasper D.Carey, Vicent J.Morgan, MartinCulhane, Aedín C.Haibe-Kains, BenjaminWaldron, Levi2017-03-292017-03-292016Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo MA et al. Public data and open source tools for multi-assay genomic investigation of disease. Briefing in Bioinformatics. 2016;17(4):603-15. DOI: 10.1093/bib/bbv0801477-4054http://hdl.handle.net/10230/28323Molecular 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.application/pdfeng© The Author 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/ ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/bib/bbv080Multiple assays (multipe-assays)Public dataBioconductorIntegrative genomicsCancerPharmacogenomicsOmicsinfo:eu-repo/semantics/openAccess