Technical services

Computing services

Siberchicot Aurélie

Ingénieure d'étude

UCBL

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 72 44 85 98

Email

University Claude Bernard Lyon 1 - Building Grégor Mendel - 1st floor - Office 51 (11.051)

 

 

As a software engineer, my work consists in designing, developing, deploying and maintaining biological data analysis tools. As an expert of the R language and software, I am in charge of many R packages which are available on CRAN, Bioconductor, GitHub and GitLab and of web applications developed with the shiny package. I am regularly associated with training and teaching modules, and I share, at these occasions, my knowledge and experience regarding the reproducibility of research and good development practices.

Evolutionary Ecology

  • ade4 (Multivariate data analysis and graphical display): CRAN -- GitHub -- book
  • ade4TkGUI (A Tcl/Tk GUI for some basic functions in the ade4 package): CRAN -- GitHub
  • adegraphics (Graphical functionalities for the representation of multivariate data): CRAN -- GitHub -- article -- talk
  • CINID (Package on the Curculionidae INstar IDentification): CRAN -- article
  • Interatrix (Compute Chi-Square Measures with Corrections): CRAN -- article
  • OnAge (Implements a likelihood ratio test of differential senescence onset between two groups): CRAN -- web

 

  • Analysis of data from the International Tiger Studbook and from the International and North American Regional Studbooks for Ruffed Lemurs -- article -- article
  • AGEX (ANR-15-CE32-0002-01, 2015-2019)  -- article
  • Potenchêne (GIP-ECOFOR, 2014-2018) -- article
  • CoCoReCo (ANR JC09-470585, 2009-2012) -- article
  • DLVitis (ANR-08-GENM-0002, 2008-2011) -- article -- CRAN

Ecotoxicology

  • GUTS-predict (General Unified Threshold Model of Survival): shiny app
  • rbioacc (Inference and Prediction of ToxicoKinetic (TK) Models): CRAN --  GitHub -- article

Bioinformatics

Statistics and data analysis

  • fitdistrplus (Help to Fit of a Parametric Distribution to Non-Censored or Censored Data): CRAN -- GitHub -- web
  • Mondrian (A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events): CRAN -- GitHub -- shiny app
  • nlsMicrobio (Nonlinear Regression in Predictive Microbiology): CRAN -- GitHub
  • nlstools (Tools for Nonlinear Regression Analysis): CRAN -- GitHub

IT services

 

Organization and Program Committee

Trainings and Courses

  • UE Visualization of Biological Data, M2 Bio-informatique, Lyon
  • Programming with R: from the simplest to the most complex, Groupe Lyon Calcul
  • Build your own package in R, ANF CNRS

Competition Jury

  • Concours externe ENS (2021) - BAP A- IE - Ingénieur·e biologiste en traitement des données
  • Concours externe INRA (2019) - Experte - BAP E - AI - Assistant·e statisticien·ne
  • Concours externe INRA (2019) - BAP E - IE - Administrateur·trice des systèmes d’information
  • Concours externe CNRS (2017) - Experte - BAP E - IE - Ingénieur·e en ingénierie logicielle - 2 postes

Supervision

  • Cassandra Bompard, stage M2, Développement d'un package R de visualisation (2023)
  • Eliane Schermer, stage M2 et thèse, Modélisation en écologie (2015-2019)
  • Luka Matsuda, stage L3, Bioinformatique, Statistique et Modélisation (2018)
  • Adrien Bessy, stage M2, Bioinformatique (2015)

Publications

Display of 1 to 21 publications on 21 in total

DRomics, a workflow to exploit dose-response omics data in ecotoxicology

Marie Laure Delignette-Muller, Aurélie Siberchicot, Floriane Larras, Elise Billoir

Peer Community Journal . 3 : e90

DOI: 10.24072/pcjournal.325

Journal article

see the publication

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

Molecular Biology and Evolution . 40 ( 11 ) : msad234

DOI: 10.1093/molbev/msad234

Journal article

see the publication

rbioacc: An R-package to analyze toxicokinetic data

Aude Ratier, Virgile Baudrot, Miléna Kaag, Aurélie Siberchicot, Christelle Lopes, Sandrine Charles

Ecotoxicology and Environmental Safety . 242 : 113875

DOI: 10.1016/j.ecoenv.2022.113875

Journal article

see the publication

Taking full advantage of modelling to better assess environmental risk due to xenobiotics

Sandrine Charles, Aude Ratier, Virgile Baudrot, Gauthier Multari, Aurélie Siberchicot, Dan Wu...

Environmental Science and Pollution Research .

DOI: 10.1007/s11356-021-15042-7

Journal article

see the publication

Lifespan decreases with proportion of sons in males but not females of zoo‐housed tigers and lemurs

Morgane Tidière, Guillaume Douay, Peter Müller, Aurélie Siberchicot, Alexander Sliwa, Mylisa Whipple...

Journal of Evolutionary Biology .

DOI: 10.1111/jeb.13793

Journal article

see the publication

Sex‐specific actuarial and reproductive senescence in zoo‐housed tiger ( Panthera tigris ): The importance of sub‐species for conservation

Morgane Tidière, Peter Müller, Alexander Sliwa, Aurélie Siberchicot, Guillaume Douay

Zoo Biology .

DOI: 10.1002/zoo.21610

Journal article

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Pollen limitation as a main driver of fruiting dynamics in oak populations

Marie-Claude Bel-Venner, David Fouchet, Aurélie Siberchicot, Vincent Boulanger, Thomas Caignard, Michel Thibaudon...

Ecology Letters . 22 ( 1 ) : 98-107

DOI: 10.1111/ele.13171

Journal article

see the publication

DRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment

Floriane Larras, Elise Billoir, Vincent Baillard, Aurélie Siberchicot, Stefan Scholz, Tesfaye Wubet...

Environmental Science and Technology . 52 ( 24 ) : 14461-14468

DOI: 10.1021/acs.est.8b04752

Journal article

see the publication

Multivariate Analysis of Ecological Data with ade4

Jean Thioulouse, Stéphane Dray, Anne-Béatrice Dufour, Aurélie Siberchicot, Thibaut Jombart, Sandrine Pavoine

DOI: 10.1007/978-1-4939-8850-1

Book

see the publication

Maternal reproductive senescence shapes the fitness consequences of the parental age difference in ruffed lemurs

Morgane Tidière, Xavier Thevenot, Adamantia Deligiannopoulou, Guillaume Douay, Mylisa Whipple, Aurélie Siberchicot...

Proceedings of the Royal Society B: Biological Sciences . 285 ( 1886 ) : 20181479

DOI: 10.1098/rspb.2018.1479

Journal article

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MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps

Aurélie Siberchicot, Adrien Bessy, Laurent Gueguen, Gabriel A. B. Marais

Genome Biology and Evolution . 9 ( 10 ) : 2506-2509

DOI: 10.1093/gbe/evx178

Journal article

see the publication

adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data

Aurélie Siberchicot, A. Julien-Laferrière, Ab. Dufour, J. Thioulouse, S. Dray

The R Journal . 9 ( 2 ) : 198-212

DOI: 10.32614/RJ-2017-042

Journal article

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Fruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies

Samuel Venner, A. Siberchicot, P.F. Pélisson, E. Schermer, Marie-Claude Bel-Venner, M. Nicolas...

The American Naturalist . 188 ( 1 ) : 66-75

DOI: 10.1086/686684

Journal article

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Unknown age in health disorders: A method to account for its cumulative effect and an application to feline viruses interactions.

Eléonore Hellard, Dominique Pontier, Aurélie Siberchicot, Frank Sauvage, David Fouchet

Epidemics . 11 : 48-55

DOI: 10.1016/j.epidem.2015.02.004

Journal article

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Determining the instar of a weevil larva (Coleoptera: Curculionidae) using a parsimonious method

A. Merville, A. Vallier, Samuel Venner, A. Siberchicot, D. Fouchet, A. Heddi...

European Journal of Entomology . 111 ( 4 ) : 567-573

DOI: 10.14411/eje.2014.056

Journal article

see the publication

Conference Report: Deuxièmes Rencontres R

Aurélie Siberchicot, S. Dray

The R Journal . 5/2 : 164--165

Journal article

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Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

Brigitte Mangin, Aurélie Siberchicot, S. Nicolas, Agnes Doligez, Patrice This, Christine Cierco-Ayrolles

Heredity . 108 ( 3 ) : 285-291

DOI: 10.1038/hdy.2011.73

Journal article

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Genetic structure and linkage disequilibrium in 4 Vitis species

Patrice This, Stephane Nicolas, Jean-Pierre Peros, Thierry Lacombe, Loic Le Cunff, Jean-Michel Boursiquot...

Plant and Animal Genomes Conference . : np

Conference paper

see the publication

Genetic structure and linkage disequilibrium in 4 Vitis species

Stephane Nicolas, Jean-Pierre Peros, Patrice P. This, Thierry Lacombe, Valerie V. Laucou, Loic L. Le Cunff...

Grapevine breeding and genetics .

Poster

see the publication

Genetic structure and linkage disequilibrium in four Vitis species

Stephane Nicolas, Jean-Pierre Peros, Patrice P. This, Thierry Lacombe, L. Le Cunff, Jean-Michel Boursiquot...

10. International Conference on Grapevine Breeding and Genetics .

Conference paper

see the publication

Genetic structure and linkage disequilibrium in 4 species of the Vitis genus

Patrice P. This, Stephane Nicolas, Alexis Dereeper, Agnès Doligez, Jean-Pierre Peros, Roberto Bacilieri...

Génoplante .

Poster

see the publication