To cite package ‘BUMHMM’ in publications use:

  Selega A, Granneman S, Sanguinetti G (2016). _BUMHMM: Computational
  pipeline for computing probability of modification from structure
  probing experiment data._. https://github.com/alinaselega/BUMHMM - R
  package version 1.29.0,
  <http://www.bioconductor.org/packages/BUMHMM>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {BUMHMM: Computational pipeline for computing probability of modification from structure probing experiment data.},
    author = {Alina Selega and Sander Granneman and Guido Sanguinetti},
    year = {2016},
    url = {http://www.bioconductor.org/packages/BUMHMM},
    note = {https://github.com/alinaselega/BUMHMM - R package version 1.29.0},
  }

  Selega A, Sirocchi C, Iosub I, Granneman S, Sanguinetti G (2016).
  “Robust statistical modeling improves sensitivity of high-throughput
  RNA structure probing experiments.” _Nature Methods_.
  doi:10.1038/nmeth.4068 <https://doi.org/10.1038/nmeth.4068>,
  <http://www.nature.com/nmeth/journal/v14/n1/full/nmeth.4068.html>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments},
    author = {Alina Selega and Christel Sirocchi and Ira Iosub and Sander Granneman and Guido Sanguinetti},
    year = {2016},
    journal = {Nature Methods},
    doi = {10.1038/nmeth.4068},
    url = {http://www.nature.com/nmeth/journal/v14/n1/full/nmeth.4068.html},
  }