Software Analysis Tools
CellHTS2
The cellHTS2 package, implemented in R/Bioconductor, provides tools for the analysis of cell-based high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). Large-scale RNAi screening with single or multi-channel raw data is imported and assembled, then analyzed with various standardization and normalization methods, annotation of data sets, and a comprehensive HTML report of the screening data analysis including per-plate and the complete screen quality assessment, replicate summarization, statistical scoring and a ranked hit list can be saved and restored for later re-analysis.
Tibco Spotfire Analytics Software
Spotfire Professional Analytics Software Suite, an integrated solution to challenges of high throughput data analysis. In the Spotfire Professional Suite data obtained from RNAi screens are gathered and integrated through the Tibco informatics infrastructure. The Suite can access primary HTS data files, perform analyses, assess data quality, integrate data with RNAi databases, generate integrated, multivariable, and multi-parametric visual reports. The Spotfire Suite comprises the following modules:
The Spotfire analytics tool offers robust data visualization and decision support against even the largest data sets. Spotfire can access local or remote data, and then filter and visualize it interactively. The software can be launched from within Lead Discovery. A key capability of the integration is that users can easily traverse between the form view of Lead Discovery and the visual analytics interface of Spotfire.
Lead Discovery provides a wealth of visualization options for exploration and analysis of chemical properties, RNAi assay results, and chemical structures. The data can be combined, visualized, and filtered. Analyses can be performed on subsets or on the entire data set to reveal trends in a compound series or from particular structural motifs, thus improving the efficiency and quality of decisions. Large datasets acquired in different screening ‘batches’ can be normalized, combined, and analyzed as a single dataset.
SciSTREAM is a generic data loader that is used to import plate-‐based data from most commercially available instruments. By directly importing raw data from multiple plates, readouts/channels, time points, as well as all relevant metadata, it is possible to analyze and compare multi-‐parametric data from many assays and experiments. Plate layout properties can be visually represented in a plate map in Spotfire, enabling scientists to interact with their data, and perform a curve fit modeling.