title: EntropyExplorer: an R package for computing and comparing differential Shannon entropy, differential coefficient of variation and differential expression.
abstract: BACKGROUND
  Differential Shannon entropy (DSE) and differential coefficient of variation (DCV) are effective metrics for the study of gene expression data. They can serve to augment differential expression (DE), and be applied in numerous settings whenever one seeks to measure differences in variability rather than mere differences in magnitude. A general purpose, easily accessible tool for DSE and DCV would help make these two metrics available to data scientists. Automated p value computations would additionally be useful, and are often easier to interpret than raw test statistic values alone.
  
  
  RESULTS
  EntropyExplorer is an R package for calculating DSE, DCV and DE. It also computes corresponding p values for each metric. All features are available through a single R function call. Based on extensive investigations in the literature, the Fligner-Killeen test was chosen to compute DCV p values. No standard method was found to be appropriate for DSE, and so permutation testing is used to calculate DSE p values.
  
  
  CONCLUSIONS
  EntropyExplorer provides a convenient resource for calculating DSE, DCV, DE and associated p values. The package, along with its source code and reference manual, are freely available from the CRAN public repository at http://cran.r-project.org/web/packages/EntropyExplorer/index.html.
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996-2250, USA. kwang11@tennessee.edu.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996-2250, USA. cphill25@tennessee.edu.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Phillips
authors.affiliation: Department of Animal Science, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996-4574, USA. asaxton@tennessee.edu.
authors.forename: Arnold M
authors.initials: AM
authors.lastname: Saxton
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996-2250, USA. langston@tennessee.edu.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Langston
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019277:Entropy; D020869:Gene Expression Profiling / Q000379:methods*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015203:Reproducibility of Results; D012984:Software