A wide range of statistical methods

One of cornerstones is the possibility to analyze data using a flexible and easy to use statistical framework. The user can select from a wide range of statistical methods, such as:  

• two group comparison (t-test, Welch or Mann-Whitney) 

• paired t –test  

• multi group comparison (ANOVA or Kruskal-Wallis) 

• two- way ANOVA 

• linear regression 

• quadratic regression 

• rank regression 

In addition to the methods above, filtering on Fold change and Log fold change (Difference) are supported. 

An Open API to R is integrated and opens for use of a wide range of other statistical methods.

The inbuilt statistical framework (a general linear statistical model) supports the handling of eliminated factors, which means that you can remove batch effects, work with paired data or even more complex experimental set-ups. 

Biomarker discovery analysis

The Biomarker Workbench is optimized for experiments and studies in the areas of drug development and biomarker discovery. Easily set up a suite of different statistical tests to run in batch mode with the objective of selecting effective compounds or other relevant signals. Add post hoc analysis including Tukey and Fold change.

Inspect the results in tables and directly use the structured outcome for the following analysis steps. The Response variable option is tailored for biomarker discovery and assists in finding correlation between sample annotations – an excellent way to focus on key annotations when working with large amounts of clinical data.

Scripted workflows

Templates is the functionality used for scripting workflows in the program. You can use built-in Templates as a quick start to standard analyses or write your own templates to simplify repetitive tasks. Templates is also the tool for integration of the program into tool chains.

Survival analysis

Survival analysis is supported with integrated statistical methods such as Hazard ratio calculations as well as visualizations in Kaplan-Meier plots.

Genome analysis

With the NGS module and the NGS filters more options are available. Select which regions of the genome to analyze in the Genome browser, dynamically select if the regions should be restricted by read coverage, specific regions or if variants should be present or not.

Cluster analysis

Clusteringis supported in several ways; either in a semi-supervised mode using PCA or t-SNE or UMAP with Projection score and variance filtering or in an unsupervised mode using kmeans++.

Classification and machine learning

The Build classifier and Classify machine learning functionality enables both the option to easily build classifiers based on models such as Boosted trees, Support Vector Machines (SVM), Random Trees (RT) and kNN and to classify new samples.

Pathway analysis

To compare and enhance your findings use the integrated GSEA Workbench which is set-up using only a few mouse-clicks. It does not get easier. Easy conversion of gene ids from different species to human orthologs is supported.

By combining the right annotations with statistical methods, data selection tools, and the eliminated factor's function, a very broad range of different experiment designs can be analyzed.

Qlucore Omics Explorer also supports analysis using:

• Hierarchical clustering
• Isomap
• The Status panel will continuously show exactly what calculations that have been applied to your data.

Read about all features in Qlucore Omics Explorer.