Package: Repitools 1.53.0

Please cite the Bioinformatics paper for the software itself and the other papers for the various original statistical methods implemented in Repitools.

Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ, Robinson MD. (2010). Repitools: an R package for the analysis of enrichment-based epigenomic data, Bioinformatics 26(13), 1662-3

Robinson MD, Strbenac D, Stirzaker C, Statham AL, Song J, Speed TP, Clark SJ (2012). Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Research 22(12):2489-96.

Riebler A, Menigatti M, Song JZ, Statham AL, Stirzaker C, Mahmud N, Mein CA, Clark SJ, Robinson MD (2014). BayMeth: Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach, Genome Biol. 15(2):R35.

Corresponding BibTeX entries:

  @Article{,
    title = {Repitools: an R package for the analysis of
      enrichment-based epigenomic data},
    author = {Statham AL and Strbenac D and Coolen MW and Stirzaker C
      and Clark SJ and Robinson MD},
    journal = {Bioinformatics},
    volume = {26},
    pages = {1659},
    year = {2010},
  }

  @Article{,
    title = {Copy-number-aware differential analysis of quantitative
      DNA sequencing data},
    author = {Robinson MD and Strbenac D and Stirzaker C and Statham AL
      and Song J and Speed TP and Clark SJ},
    journal = {Genome Research},
    volume = {22},
    pages = {2393},
    year = {2012},
  }

  @Article{,
    title = {BayMeth: Improved DNA methylation quantification for
      affinity capture sequencing data using a flexible Bayesian
      approach},
    author = {Riebler A and Menigatti M and Song JZ and Statham AL and
      Stirzaker C and Mahmud N and Mein CA and Clark SJ and Robinson
      MD},
    journal = {Genome Biology},
    year = {2014},
    volume = {15},
    pages = {R35},
  }