https://github.com/cbrueffer/mutationexplorer

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

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

Last synced: 24 days ago
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R Shiny based lightweight mutation exploration tool

• Host: GitHub
• URL: https://github.com/cbrueffer/mutationexplorer
• Owner: cbrueffer
• License: bsd-2-clause
• Created: 2018-10-29T22:51:06.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2021-03-04T09:29:17.000Z (over 3 years ago)
• Last Synced: 2023-04-01T10:22:44.259Z (over 1 year ago)
• Topics: bioinformatics, cancer, cancer-genomics, mutations, rna-seq, scanb, shinyapp, somatic-mutations
• Language: R
• Size: 354 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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)