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Creating and Comparing Cohorts

Data Analysis is the ultimate goal of all pipelines, laying the foundation for getting early actionable insights for drug discovery and biomarker validation.

Quark's intuitive interface accelerates biomarker discovery and validation by simplifying the user's experience of exploratory data analysis.

Analytics Overview

The results of all Pipeline Runs are consolidated and retrievable through a single Analytics tab.

Quark Analytics is where users can perform their tertiary data analysis or exploratory data analysis. Users can view the results of their pipeline runs to Build Cohorts, and Run Cohort Comparisons.

Additionally, users can generate specialised plots and graphs to view their analyses using Quark's visualisation tools.

To perform exploratory data analysis, select Analytics from the Navigator pane to the left of the Quark screen, which displays the following tabs:

  • Cohorts: Users can create cohorts, view the cohorts they have built, and easily run cohort comparisons with a single-click API from this tab.

  • Analyses: Users can view the results of their cohort comparisons from this tab. The analyses tab provides a comprehensive list of visualisation tools.

Exploratory data analysis requires a comprehensive toolkit that simplifies cohort creation, and cohort comparison. Quark provides analytical tools that include graphics for easier visualisation, for both cohort creation and cohort comparisons.

Creating and Comparing Cohorts

Cohort creation is a crucial step in exploratory data analysis, where patients are stratified into groups based on their phenotypic or genotypic features. This is necessary for cohort comparisons in tertiary data analysis where biomarkers related to a disease condition are identified.

Creating Cohorts

  • Select Analytics from the Navigator Pane on the left.
  • Select the tab labeled Cohorts, and click on the Add New button on the top right.
  • The Analytics window opens to a page where users can retrieve results based on their Pipeline. Select the relevant pipeline from the drop-down menu.
  • Select the prompted Genome from the drop-down.
  • Use the Search option to filter all Run results unified on the analytics tab. Follow the prompts to stratify patients based on genotypic or phenotypic features. (e.g., input a comma-separated list of genes to stratify patients based on the gene of interest)
  • Select Search. The window opens to the Sample table, a Summary (for each gene), and Plots that displays metadata characteristics for the sample.
  • Patient cohorts can be built to identify biomarkers specific to a genotypic or phenotypic trait (such as a treated vs. untreated cohort or normal vs. tumour samples)
  • To create a cohort, for example, of treated patient samples, sort the sample data based on Status to find your patients of interest. Select Save and name the cohort.
  • Create as many cohorts as required for the study based on your project needs.

Comparing Cohorts

  • Once cohorts have been created, cohort comparison is done on the main Analytics page. Select Analytics from the left Navigator Menu, and select the Cohorts tab.
  • Cohorts created in the previous step will be displayed on this page.
  • Select the cohorts of interest that need to be compared by selecting '+' next to them.
  • The bottom pop up Panel displays the names of the cohorts.
  • Confirm the input and run the comparison analysis by clicking Compare.
  • Name the comparison analysis and provide a description. Click Submit.
  • Once cohort comparison analysis is completed, the results will be displayed under the Analyses tab.
  • Details of the comparison analyses will be shown, such as the Status of the analysis, type of Analysis (like RNA Sequencing or DNA Sequencing) and names of the Cohorts compared.
  • Access the results of your cohort comparison by clicking the chart icon next to your run. This will take you to the results of your tertiary data analysis.