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R Shiny based lightweight mutation exploration tool
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README.md

MutationExplorer

MutationExplorer is a lightweight web application for exploring somatic mutations in cancer datasets. It is based on R and the Shiny framework.

MutationExplorer is currently most usable for breast cancer samples, since the relevant biomarkers for patient selection (e.g. clinical status of ER and PgR) are hardcoded.

Features

  • Filtering of mutations by type (nonsense, missense, etc) and COSMIC status
  • Filtering of the patient sample cohort by histological/genomic biomarker status
  • Mutational landscape waterfall plots
  • Kaplan-Meier survival analysis based on gene and pathway mutation status, as well as tumor mutation burden (TMB)
  • Protein plots similar to cBioPortal oncoprints or lollipop plots

Authors

This software was developed as part of a PhD research project in the laboratory of Lao H. Saal, Translational Oncogenomics Unit, Department of Oncology and Pathology, Lund University, Sweden.

Availability

A MutationExplorer instance with the data from 3,217 primary breast tumor transcriptomes from the Sweden Cancerome Analysis Network--Breast (SCAN-B) can be accessed at https://oncogenomics.bmc.lu.se/MutationExplorer.

Citation

Brueffer et al (2020). The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome. bioRxiv. DOI: 10.1101/2020.01.30.926733

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