Gene chip databases already serve as transcriptomic basis for cross-dataset analysis tools like Breast-Mark [ 36] or the KM-plotter [ 37].
To assure long-term up-to-date datasets and analysis tools, GeneReporter utilizes standardized web services from the EBI (Goujon et al., 2010), the NCBI (Sayers et al., 2010) and our institute.
The significance of this approach is that urban geographers can access both the datasets and statistical analysis tools via the same online Portal and thus in theory, conduct their research more efficiently.
To verify the clinical relevance of YAP up-regulation in the cervical cancer, we performed a cross-cancer YAP gene alteration analysis by using the multidimensional cancer genomic datasets and online analysis tools.
We here present CNVineta, an R package capable of handling CNV data derived from large datasets with implemented analysis tools for the detection and visualization of disease-associated rare (Supplementary Fig. S4) and common CNVs (Supplementary Figs S5, S6).
Therefore, our goal was to develop a tool suite that facilitates exploration and analysis of large-scale genomic and proteomic datasets and that provides means to easily identify and exchange the underlying datasets used by the analysis tools.
Chipster's user interface consists of four panels: Analysis tools, datasets, workflow and visualization.
The framework's components help manage data flow between Web browser and Web server, provide methods for indexing and quickly obtaining data from large genomic datasets, integrate visualization and analysis tools, and enable sharing and publication of saved visualizations.
For example, our analysis of interneuron firing indicates that while E-I models predict that interneurons will have spatial firing fields, they have lower spatial information content, spatial sparsity and grid scores than E cells and therefore may be difficult to detect in existing experimental datasets and with current analysis tools.
HUBzero can handle a variety of data types including documents created with Microsoft Office©, PDFs, ASCII files, images and video clips, analysis tools, and datasets.
