Qlucore, a developer of bioinformatics software, has unveiled Qlucore Omics Explorer 3.0, the latest version of its analysis software.
The software includes two new integrated tools that focus on facilitating the analysis of data by comparing how the experiment corresponds to public information and results.
The new GO browser allows users to search within any ontology; interesting results can then be exported to the variable window and used as a normal variable list.
Gene Set Enrichment Analysis workbench (GSEA) provides a complete set of results for large data sets (132 x 50,000) with just three mouse clicks, and in less than 30 seconds.
The new functionality allows scientists to view all elements of a specific list in a dedicated colour in all open plots. This is designed to aid the scientist in interpreting the combination of their own experiment against publically available information.
In the past many scientists have had to overcome the problem of working with identifiers for variables in public data being different from those used in their own experiments. This has made their work complicated and tedious when comparing information. The new Qlucore Omics Explorer 3.0 aims to solve this problem by introducing the variable collapse function.
The variable collapse function is used for data sets with multiple measurements for the same variable. A typical example is for gene expression microarrays where you measure several probes or features that match to one gene. Using the variable collapse you can either study data at gene level or probe/feature level.
In addition, the projection score system has been introduced, which provides the user with information on how well the visual representation actually represents the data. The projection score measures how informative a low-dimensional representation obtained by PCA is. It also provides explicit comparison of representations corresponding to different variable subsets.
The new file import functionality for aligned RNA-seq (BAM files) will make it easier for users who want to analyse digital gene expression data. Once the files are imported everything else is done automatically, with easy access to all Qlucore Omics Explorer analysis functionality. These include: heatmap with hierarchical clustering, PCA plots, fold change filtering, GSEA analysis and Anova analysis.