Literature DB >> 24976799

isocir: An R Package for Constrained Inference using Isotonic Regression for Circular Data, with an Application to Cell Biology.

Sandra Barragán1, Miguel A Fernández2, Cristina Rueda3, Shyamal Das Peddada4.   

Abstract

In many applications one may be interested in drawing inferences regarding the order of a collection of points on a unit circle. Due to the underlying geometry of the circle standard constrained inference procedures developed for Euclidean space data are not applicable. Recently, statistical inference for parameters under such order constraints on a unit circle was discussed in Rueda et al. (2009); Fernández et al. (2012). In this paper we introduce an R package called isocir which provides a set of functions that can be used for analyzing angular data subject to order constraints on a unit circle. Since this work is motivated by applications in cell biology, we illustrate the proposed package using a relevant cell cycle data.

Entities:  

Keywords:  CIRE; Circular Data; Circular Order; Conditional Test; R; R package isocir

Year:  2013        PMID: 24976799      PMCID: PMC4070741          DOI: 10.18637/jss.v054.i04

Source DB:  PubMed          Journal:  J Stat Softw        ISSN: 1548-7660            Impact factor:   6.440


  11 in total

1.  A random-periods model for expression of cell-cycle genes.

Authors:  Delong Liu; David M Umbach; Shyamal D Peddada; Leping Li; Patrick W Crockett; Clarice R Weinberg
Journal:  Proc Natl Acad Sci U S A       Date:  2004-05-03       Impact factor: 11.205

2.  Migrating songbirds recalibrate their magnetic compass daily from twilight cues.

Authors:  William W Cochran; Henrik Mouritsen; Martin Wikelski
Journal:  Science       Date:  2004-04-16       Impact factor: 47.728

3.  Co-evolution of transcriptional and post-translational cell-cycle regulation.

Authors:  Lars Juhl Jensen; Thomas Skøt Jensen; Ulrik de Lichtenberg; Søren Brunak; Peer Bork
Journal:  Nature       Date:  2006-09-27       Impact factor: 49.962

4.  Identification of cell cycle-regulated genes in fission yeast.

Authors:  Xu Peng; R Krishna Murthy Karuturi; Lance D Miller; Kui Lin; Yonghui Jia; Pinar Kondu; Long Wang; Lim-Soon Wong; Edison T Liu; Mohan K Balasubramanian; Jianhua Liu
Journal:  Mol Biol Cell       Date:  2004-12-22       Impact factor: 4.138

5.  Circadian clock gene expression in brain regions of Alzheimer 's disease patients and control subjects.

Authors:  Nicolas Cermakian; Elaine Waddington Lamont; Philippe Boudreau; Diane B Boivin
Journal:  J Biol Rhythms       Date:  2011-04       Impact factor: 3.182

6.  Estimation of Parameters Subject to Order Restrictions on a Circle With Application to Estimation of Phase Angles of Cell Cycle Genes.

Authors:  Cristina Rueda; Miguel A Fernández; Shyamal Das Peddada
Journal:  J Am Stat Assoc       Date:  2009-03-01       Impact factor: 5.033

7.  Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species.

Authors:  Miguel A Fernández; Cristina Rueda; Shyamal D Peddada
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

8.  Phase analysis of circadian-related genes in two tissues.

Authors:  Delong Liu; Shyamal D Peddada; Leping Li; Clarice R Weinberg
Journal:  BMC Bioinformatics       Date:  2006-02-23       Impact factor: 3.169

9.  The cell cycle-regulated genes of Schizosaccharomyces pombe.

Authors:  Anna Oliva; Adam Rosebrock; Francisco Ferrezuelo; Saumyadipta Pyne; Haiying Chen; Steve Skiena; Bruce Futcher; Janet Leatherwood
Journal:  PLoS Biol       Date:  2005-06-28       Impact factor: 8.029

10.  Periodic gene expression program of the fission yeast cell cycle.

Authors:  Gabriella Rustici; Juan Mata; Katja Kivinen; Pietro Lió; Christopher J Penkett; Gavin Burns; Jacqueline Hayles; Alvis Brazma; Paul Nurse; Jürg Bähler
Journal:  Nat Genet       Date:  2004-06-13       Impact factor: 38.330

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  1 in total

1.  Isotonic regression for metallic microstructure data: estimation and testing under order restrictions.

Authors:  Martina Vittorietti; Javier Hidalgo; Jilt Sietsma; Wei Li; Geurt Jongbloed
Journal:  J Appl Stat       Date:  2021-03-05       Impact factor: 1.416

  1 in total

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