GMD: measuring the distance between histograms with applications on high-throughput sequencing reads

Bioinformatics. 2012 Apr 15;28(8):1164-5. doi: 10.1093/bioinformatics/bts087. Epub 2012 Feb 17.

Abstract

GMD (generalized minimum distance of distributions) is an R package to assess the similarity between spatial distributions of read-based sequencing data such as ChIP-seq and RNA-seq. GMD calculates the optimal distance between pairs of normalized signal distributions, optionally sliding one distribution over the other to 'align' the distributions. GMD also provides graphical and downstream clustering tools.

Availability: The R package GMD source code is available at http://cran.r-project.org/web/packages/GMD/ under GPL license.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Immunoprecipitation / methods
  • High-Throughput Nucleotide Sequencing*
  • Histone Code
  • Histones / metabolism
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA
  • Software*
  • Transcription Initiation Site

Substances

  • Histones