Technical services

Computing services

Siberchicot Aurélie

Ingénieure de recherche

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 core activity is to develop and maintain data analysis software to enhance and sustain research results. As an expert in the R language and its ecosystem, I am responsible for numerous R packages and shiny apps. To share my R-related skills, I design original training courses and take part in teaching programs. More broadly, I'm interested in tools for reproducible research and open science.

  • Position and responsibilities
    • Research Engineer, Normal Class, since 2023
    • Representative of the LBBE IT Department, since 2018
    • ITA / BIATSS representative on the UMR council, since 2017
  • Networks and IDs

Evolutionary Ecology

  • ade4 (Multivariate data analysis and graphical display) : CRAN -- GitHub -- book -- shiny app
  • 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
  • adephylo (Exploratory Analyses for the Phylogenetic Comparative Method) : CRAN --  GitHub
  • adespatial (Multivariate Multiscale Spatial Analysis) : CRAN -- GitHub
  • 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

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

 

Professional networks and conferences

Trainings and Courses

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 22 publications on 22 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

Larval density in the invasive Drosophila suzukii : Immediate and delayed effects on life‐history traits

Alicia Reyes‐ramírez, Zaïnab Belgaidi, Patricia Gibert, Thomas Pommier, Aurélie Siberchicot, Laurence Mouton...

Ecology and Evolution . 13 ( 8 ) : e10433

DOI: 10.1002/ece3.10433

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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