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

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

Author information

  • 1Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, Copenhagen University, Copenhagen, Denmark. xiaobei@binf.ku.dk

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.

PMID:
22345619
[PubMed - indexed for MEDLINE]
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