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https://github.com/cbrueffer/mutationexplorer

R Shiny based lightweight mutation exploration tool
https://github.com/cbrueffer/mutationexplorer

bioinformatics cancer cancer-genomics mutations r rna-seq scanb shiny shinyapp somatic-mutations

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R Shiny based lightweight mutation exploration tool

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# 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](https://cancer.sanger.ac.uk/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

- Christian Brueffer ([@cbrueffer](http://github.com/cbrueffer/))
- Sergii Gladchuk ([@sergiigladchuk](http://github.com/sergiigladchuk/))

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](https://www.med.lu.se/saalgroup).

## Availability

A MutationExplorer instance with the data from 3,217 primary breast tumor transcriptomes from the [Sweden Cancerome Analysis Network--Breast (SCAN-B)](https://portal.research.lu.se/portal/en/projects/sweden-cancerome-analysis-network--breast-scanb-a-largescale-multicenter-infrastructure-towards-implementation-of-breast-cancer-genomic-analyses-in-the-clinical-routine%2898b7c09f-85d5-4f98-bcae-a43bffb6f869%29/publications.html) 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. EMBO Molecular Medicine, 12(10):e12118. DOI: [10.15252/emmm.202012118](https://doi.org/10.15252/emmm.202012118)