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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
Last synced: 5 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 (almost 4 years ago)
- Last Synced: 2024-10-31T02:41:31.373Z (about 2 months ago)
- Topics: bioinformatics, cancer, cancer-genomics, mutations, r, rna-seq, scanb, shiny, shinyapp, somatic-mutations
- Language: R
- Homepage:
- Size: 354 KB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
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)