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

Bioinformatics
Xiaobei Zhao, Albin Sandelin

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

References

Apr 29, 2006·Nature Genetics·Piero CarninciYoshihide Hayashizaki
Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
Aug 9, 2011·Nature Structural & Molecular Biology·Eivind ValenTorben Heick Jensen
Sep 3, 2011·PloS One·Xiaobei ZhaoAlbin Sandelin

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Citations

Oct 23, 2012·European Journal of Oncology Nursing : the Official Journal of European Oncology Nursing Society·Ulrika FallbjörkPär Salander
Aug 5, 2016·Agriculture, Ecosystems & Environment·Job KiharaJeroen Huising
Jun 12, 2016·Behavior Research Methods·Alexandra C ConstantinescuSarah E MacPherson
Nov 25, 2016·Environmental Microbiology·Koji YaharaSamuel K Sheppard
Aug 28, 2020·NPJ Systems Biology and Applications·Matteo ManicaPavel Sumazin
Dec 9, 2017·Briefings in Bioinformatics·Brian B LuczakHani Z Girgis
Oct 19, 2019·Ecology and Evolution·Anna Voulgari-KokotaAlexander Keller

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