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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
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[![DOI: 10.1093/nar/gkaa120](https://zenodo.org/badge/doi/10.1101/853150.svg)](https://doi.org/10.1101/853150)
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*DecompPipeline* provides a comprehensive list of preprocessing functions for performing reference-free deconvolution of complex DNA methylation data. It is an integral part of a recently published protocol [doi:10.1101/853150](https://doi.org/10.1101/853150) for reference-free deconvolution and is independent of the deconvolution tool used.
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*DecompPipeline* provides a comprehensive list of preprocessing functions for performing reference-free deconvolution of complex DNA methylation data. It is an integral part of a recently published [protocol](https://www.nature.com/articles/s41596-020-0369-6) for reference-free deconvolution and is independent of the deconvolution tool used.
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![Overview of the reference-free deconvolution tool](pictures/protocol_overview.png)
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## Combining the above steps
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We also provide a wrapper functions that executes all the above steps in a single command (```start_decomp_pipeline```).
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# Citation
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If you use *DecompPipeline*, please cite:
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Scherer, M., Nazarov, P. V., Toth, R., Sahay, S., Kaoma, T., Maurer, V., Vedeneev, N., Plass, C., Lengauer, T., Walter, J., & Lutsik, P. (2020). Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz. Nature Protocols, 15(10), 3240–3263. https://doi.org/10.1038/s41596-020-0369-6

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