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Since then, the TCGA initiative has greatly expanded the number of patients, the volume of data and the diversity of analytical platforms used.
Although studies as those reported in (Curtis et al., 2012), and other large-scale integrative analyses using the TCGA (Cooper et al., 2012; Setty et al., 2012; TCGA Research Network, 2008; TCGA Research Network, 2011; Zeeberg et al., 2012), themselves make use of broad datasets, their results are often the starting point for further study of the numerous biomolecular bases for tumorigenesis.
These data types include gene expression, single-nucleotide polymorphism, mi RNA, copy number, DNA methylation and somatic mutations, along with tissue slide images and clinical outcomes.
Since 2011, this data has been available via an HTTP repository ( Jac).
They also present a much more interoperable and reproducible alternative to the still pervasive use of data portals. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data.
Availability: A prepared dashboard, including links to source code and a SPARQL endpoint, is available at Alternatively, you can download the file locally and open with any standalone PDF reader: https://bioinformatics.oxfordjournals.org/content/29/10/1333pdf Advance Access publication April A self-updating road map of The Cancer Genome Atlas David E. However, to realize this possibility, a continually updated road map of files in the TCGA is required.
The need to navigate through data portals, such as reported in (Zhang et al., 2011a) or download bulk data prevents programmatic exploration of the contents of the TCGA, hampering the leveraging of this wealth of data in point-of-care scenarios.