github.com/stianlagstad/chimeraviz ↗
chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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Contributors
9
Lines of Code
1,343
From
2016-11-25
To
2021-01-16
About stianlagstad/chimeraviz
chimeraviz is an R package designed to automate the visualization of chimeric RNA, which are fusion transcripts that combine sequences from two different genes. The package simplifies the analysis workflow by supporting import from twelve different fusion-detection tools including deFuse, FusionCatcher, STAR-FUSION, and others, allowing researchers to work with outputs from their preferred computational pipeline and generate standardized visualizations.
The package has been widely adopted in cancer genomics research, with citations spanning applications in dermatofibrosarcomas, sarcomas, prostate cancer, glioblastoma, and other malignancies. Its utility extends to both basic research exploring novel fusion genes and clinical applications where fusion status is relevant for patient stratification and prognosis. The project originated as a master's thesis and was published as an application note in Oxford Bioinformatics.
Development is supported through Docker and Conda environments for easier setup and contribution. The package includes a comprehensive test suite using testthat and is available on Bioconductor. It is distributed under the Artistic Licence 2.0, making it freely available for both academic and commercial use.