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CpelNano

MIT license

Description

CpelNano is the first method designed to perform DNA methylation differential analysis using nanopore sequencing data. The package is based on a recently published method [1]. CpelNano not only detects mean methylation level differences between groups and pairs of samples, but it can also detect significant differences in methylation entropy as well as in the probability distribution of methylation (see [1] for technical details).

Testing

CpelNano is tested against Julia 1.3.0 on the latest versions of Linux, macOS and Windows.

Getting Started

Prerequisites

  • julia v1.3.0
  • git.

Installing

CpelNano and dependencies can be installed via the following command in julia's REPL:

(v1.3) pkg> add https://github.com/jordiabante/CpelNano.jl.git

Running the tests

In order to test the package to ensure that it has been properly installed, run the following command in a julia session:

(v1.3) pkg> test CpelNano

If the package has been properly installed, then all tests will be successful.

Authors

  • Jordi Abante
  • Sandeep Kambhampati

License

This project is licensed under the MIT License - see the LICENSE.md file for details.

References

[1] Abante, J., Kambhampati, S., Feinberg, A.P., Goutsias, J., Estimating DNA methylation potential energy landscapes from nanopore sequencing data. bioRxiv (2021).

[2] Abante, J., Kambhampati, S., Feinberg, A.P., Goutsias, J., Estimating DNA methylation potential energy landscapes from nanopore sequencing data. Scientific Reports (2021), 11-21619.