Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores.

Bioinformatics
Jasmina BogojeskaJörg Rahnenführer

Abstract

In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.

References

Jan 10, 2003·Nucleic Acids Research·Soo-Yon RheeRobert W Shafer
Jan 20, 2005·Bioinformatics·Niko BeerenwinkelThomas Lengauer
Feb 12, 2005·Bioinformatics·Jörg RahnenführerThomas Lengauer
May 5, 2005·The Journal of Infectious Diseases·Niko BeerenwinkelRolf Kaiser
Aug 20, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Niko BeerenwinkelThomas Lengauer
Jun 9, 2007·International Journal of Cancer. Journal International Du Cancer·Ralf KetterJörg Rahnenführer
Mar 28, 2008·BMC Bioinformatics·Jasmina BogojeskaJörg Rahnenführer

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Citations

Apr 8, 2009·Journal of Neural Transmission·Teresa BiermannStefan Bleich
Jan 16, 2010·Molecular Biotechnology·Philippe Collas
Aug 14, 2012·Biometrical Journal. Biometrische Zeitschrift·Katrin HainkeRoland Fried
Feb 14, 2017·Nature Reviews. Genetics·Russell Schwartz, Alejandro A Schäffer
Feb 6, 2018·Glia·Hélène HirbecFrançois Rassendren
May 22, 2018·Biotechnology Journal·Davide Vito, Christopher Mark Smales
May 23, 2019·Science Advances·Nora ScarcelliYves Vigouroux
Feb 8, 2019·BMC Plant Biology·Monika SkorupaJarosław Tyburski
Feb 17, 2019·Nature Communications·Fu-Ping ZhangJorma J Palvimo
Oct 3, 2019·Proceedings. Biological Sciences·Evan L MacLeanJames A Serpell
Apr 10, 2019·Proceedings. Biological Sciences·Peter R TeskeLuciano B Beheregaray
Apr 6, 2019·BMC Genomics·Joseph L SevignyW Kelley Thomas
Apr 16, 2020·BMC Genomics·Felix P FreyFrank Hochholdinger
Jul 7, 2016·Genome Biology·Evelien M BunnikKarine G Le Roch
Aug 24, 2018·Scientific Reports·Vittoria RoncalliPetra H Lenz
Feb 7, 2018·Interdisciplinary Sciences, Computational Life Sciences·Agnieszka Cecotka, Joanna Polanska
Apr 21, 2020·Molecular Ecology·Cait A McDonaldKelly R Zamudio

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Software Mentioned

Mtreemix
Rtreemix
R package
R
LEDA
Bioconductor

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