iTReX: interactive Therapy Response eXploration v1.3.0


What is iTReX?

iTReX provides a complete workflow for analyzing therapy responses through five main functional modules:
  • The Quality Control and Normalization module (QCN-mod).
  • The Mono-therapy Response Analysis module (MRA-mod).
  • The Combination therapy Response Analysis module (CRA-mod).
  • The drug Hits interaction Network mapping module (HitNet-mod).
  • A module for identifying potential sample-specific omics-based biomarkers from drug target connectivity networks (Omics-mod).
Step-by-step instructions can be found in the iTReX User Manual.

Required Input Files


Optional Input Files
  • iTReX can compute selective scores if reference sample(s) are available.
  • Please check the box below to upload the reference sample(s) spreadsheet (optional). The reference sample(s) must by analyzed first using iTReX, The DSS_asym scores must be used to compute the mean of multiple reference samples and the spreadsheet should be with the same format as the available demo below:
  • Reference Sample(s)
  • Please note that the therapy names must match the uploaded therapies specified in the screen layout, any mismatched therapy names will be ignored and computed as NA [NB: Naming is case sensitive].

Analysis Parameters


Start of Analysis

Please upload all required input files to continue.
Please head to the QCN-mod tab to start your analysis.











About iTReX

iTReX is an R/Shiny web application for interactive analysis, visualization and exploration of mono- and combination therapy dose response profiling data and drug target interaction network mapping. iTReX features an extended version of the drug sensitivity score (DSS_asym), integrating an advanced five-parameter logistic dose-response curve model and a differential drug sensitivity score (dcDSS) for combination therapy profiling.

License information

The iTReX source code is available on GitHub and licensed under the GNU General Public License v3.0.

Disclaimer

The use of the app is purely for research purposes.

The application is under development and might be subject to changes. It has not been verified and has not been clinically validated.

Use of the provided results for diagnostic or therapy stratification or any implementation of the results in a clinical setting is in the sole responsibility of the treating physician and/or user.

The user is responsible for the quality of the uploaded data and ensures that data do not contain any personal data.

Privacy

Further information about our Terms of Use and Data Protection Policy can be found in English or in German.

Version information

We follow semantic versioning: changes in the first digit of the version number (e.g., v1.1.1) indicate major updates potentially with different result outputs. Changes in the second digit (e.g., v1.1.1) indicate added features, while changes in the third digit (e.g., v1.1.1) indicate patches and bug fixes.

Contact

In case of any questions, feel free to open an issue on GitHub or contact us via email at ✉ itrex@dkfz-heidelberg.de.

Contribution

iTReX was developed in a collaboration between the groups of

  • Translational Pediatric Pharmacology, Clinical Cooperation Unit Pediatric Oncology (Dr. Sina Oppermann) and
  • Bioinformatics and Omics Data Analytics (Prof. Dr. Matthias Schlesner)
at the Hopp Children's Cancer Center (KiTZ) and the German Cancer Research Center (DKFZ), Heidelberg, Germany.

Authors: Dina ElHarouni, Yannick Berker (Programmers), Sina Oppermann, Matthias Schlesner

How to cite

ElHarouni D, Berker Y, …, Schlesner M, Oppermann S (2022). iTReX: Interactive exploration of mono- and combination therapy dose response profiling data. Pharmacological Research, 175, 105996. https://doi.org/10.1016/j.phrs.2021.105996

iTReX usage

iTReX is currently being used in the following projects:

  • COMPASS (Clinical implementation Of Multidimensional PhenotypicAl drug SenSitivities in paediatric precision oncology)
  • UNITE Glioblastoma (Understanding and Targeting Resistance in Glioblastoma)