Welcome to CRUX’s documentation!

CRUX is a tool for analysing somatic cancer datasets at the cohort level.

Crux can be used to

1. Identify Candidate Cancer Drivers

2. Compare Genomics of Two Cohorts of Cancer

3. Examine Cohort-Level Patterns in Mutational Signatures

4. Investigate how clinical metadata are associated with cancer genomics

See Using CRUX for how to perform these analyses.

What is CRUX

CRUX is a tool for exploring cancer cohort next-generation sequencing datasets (primarily WGS & WES)

Table Of Contents

• Installing CRUX
  • Windows
  • Mac
  • Linux
• Using CRUX
  • Choosing your dataset
  • Single Cohort Mode
  • Two-Cohort Mode
  • Subsetting and Merging Cohorts
• Importing Custom Datasets
  • Step 1: Preparing your mutation data
  • Step 2: Prepare Clinical Annotation Files
  • Step 3: Importing your dataset into CRUX
  • Annotating Variants with VEP (Graphical tools only)
  • Data Dictionaries
• Appendix
  • Recreating analyses from the CRUX manuscript
  • New and Additional Studies
• FAQ
  • Data Import
  • Analysis
  • Tool development
  • Miscellaneous
• Acknowledgements

Where to get help

For help with using CRUX, please contact us.

We would be happy to set up a virtual meeting to provide a live demo of the tool or help resolve issues.

Funding

This project was supported by grant 1165556 awarded through the 2018 Priority-driven Collaborative Cancer Research Scheme and co-funded by Cancer Australia and My Room. We would also like to acknowledge Luminesce Alliance – Innovation for Children’s Health for its contribution and support. Luminesce Alliance, is a not-for-profit cooperative joint venture between the Sydney Children’s Hospitals Network, the Children’s Medical Research Institute, and the Children’s Cancer Institute. It has been established with the support of the NSW Government to coordinate and integrate paediatric research. Luminesce Alliance is also affiliated with the University of Sydney and the University of New South Wales Sydney.