Siberchicot Aurélie
Ingénieure de recherche
UCBL
aurelie.siberchicot@univ-lyon1.fr
University Claude Bernard Lyon 1 - Building Grégor Mendel - 1st floor - Office 51 (11.051)
As a software engineer, my core activity is to design, 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 bespoke training courses around R and its tools, and I regularly take part in teaching programs. More broadly, I'm committed to reproducible research and am involved in the opening up of code and software as vehicles of transparency, collaboration and sustainability in scientific practices.
- Networks and IDs
- GitHub: aursiber
- ORCID: 0000-0002-7638-8318
- HAL: aurelie-siberchicot
- Google Scholar
- Position and responsibilities
- Scientific Research Engineer (Ingénieure de Recherche) since 2023
- Scientific Project Engineer (Ingénieure d'Études) from 2012 to 2023
🧰 Modelling & Scientific Analysis Tools
Multivariate, Spatial & Phylogenetic Analysis
- 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
- Interatrix (Compute Chi-Square Measures with Corrections): CRAN -- article
- Mondrian (A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events): CRAN -- GitHub -- shiny app
Non-Linear Statistics & Distributions
- aods3 (Analysis of Overdispersed Data using S3 Methods): CRAN -- GitHub
- fitdistrplus (Help to Fit of a Parametric Distribution to Non-Censored or Censored Data): CRAN -- GitHub -- web
- nlsMicrobio (Nonlinear Regression in Predictive Microbiology): CRAN -- GitHub
- nlstools (Tools for Nonlinear Regression Analysis): CRAN -- GitHub
🧬 Bioinformatics & Functional Genomics
- DRomics (Dose Response for Omics): CRAN -- GitHub -- web -- shiny app 1 -- IFB cloud appliance 1 -- shiny app 2 -- IFB cloud appliance 2 -- poster -- article1 -- article2
- kissDE (Retrieves Condition-Specific Variants in RNA-Seq Data): Bioconductor -- GitHub
- LDcorSV (Linkage Disequilibrium Corrected by the Structure and the Relatedness): CRAN -- article
- LifemapR (Data Visualisation on 'Lifemap' Tree): CRAN -- GitHub
- MareyMap (Estimation of Meiotic Recombination Rates Using Marey Maps): CRAN -- GitHub -- web -- shiny app -- article
- phylter (Detect and Remove Outliers in Phylogenomics Datasets): CRAN -- GitHub
- ssd4mosaic (Web Application for the SSD Module of the MOSAIC Platform): CRAN -- GitLab
🧪 Applications in Ecology & Biology
- CINID (Curculionidae INstar IDentification): CRAN -- article
- OnAge (Test of Between-Group Differences in the Onset of Senescence): CRAN -- web
- WindiApp (Assessment of the risk of wind dispersal of Culicoides): shiny app
🧭 Research Projects (software contribution)
- 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 (JC09-470585, 2009-2012) -- article
🌐 Online Platforms & Resources
- GitLab and GitHub organizations of LBBE
- shiny serveur: http://lbbe-shiny.univ-lyon1.fr
- Website of Statistics in Biology: http://pbil.univ-lyon1.fr/R/
Professional Networks & Conferences
- Rencontres R (Steering Committee, since 2023)
- 3e Journées Nationales du Réseau de la Recherche Reproductible (Conference, Organization Committee, Lyon, 2025)
- 7e Rencontres R (Conference, Programm Committee, Rennes, 2018)
- R pour le calcul (Action Nationale de Formation CNRS, Organization Committee, Aussois, 2015)
- 2e Rencontres R (Conference, Organization Committee, Lyon, 2013) -- article
Trainings & Courses
- UE IT Bases, M1 Biodiversité, Écologie et Évolution, University Lyon 1, since 2022
- UE Visualization of Biological Data, M2 Bio-informatique, University Lyon 1, since 2019
- Reproducible Research in Computational Ecology, FRB-Cesab et Gdr Ecostat, since 2022
- The basics of the R language, University Savoie Mont Blanc, from 2022 to 2024
- Programming with R: from the simplest to the most complex, Groupe Lyon Calcul, 2018
- Build your own R package, ANF CNRS R pour le calcul, 2015
Competition Jury
- Concours externe CNRS (2025) - BAP E- IR - Expert·e en calcul scientifique
- 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
Student 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 30 publications on 37 in total
Windi App, an R Shiny Tool to Rapidly Assess the Risk of Culicoides Wind Dispersal
13. International Congress for Veterinary Virology Including an EPIZONE Session .
Poster
see the publicationfitdistrplus: Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
Software
see the publicationade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Software
see the publicationDRomics, a workflow to exploit dose-response omics data in ecotoxicology
Peer Community Journal . 3 : e90
Journal article
see the publicationLarval density in the invasive Drosophila suzukii : Immediate and delayed effects on life‐history traits
Ecology and Evolution . 13 ( 8 ) : e10433
DOI: 10.1002/ece3.10433
Journal article
see the publicationPhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets
Molecular Biology and Evolution . 40 ( 11 ) : msad234
Journal article
see the publicationrbioacc: An R-package to analyze toxicokinetic data
Ecotoxicology and Environmental Safety . 242 : 113875
Journal article
see the publicationTaking full advantage of modelling to better assess environmental risk due to xenobiotics
Environmental Science and Pollution Research .
Journal article
see the publicationLifespan decreases with proportion of sons in males but not females of zoo‐housed tigers and lemurs
Journal of Evolutionary Biology .
DOI: 10.1111/jeb.13793
Journal article
see the publicationSex‐specific actuarial and reproductive senescence in zoo‐housed tiger ( Panthera tigris ): The importance of sub‐species for conservation
Zoo Biology .
DOI: 10.1002/zoo.21610
Journal article
see the publicationUtilisation de DRomics pour modéliser les données omiques de type dose-réponse dans le cadre de l’appréciation du risque environnemental
SEFA (Société d’Ecotoxicologie Fondamentale et Appliquée) .
Conference paper
see the publicationDRomics: an R tool for modelling omics dose-response data
Congrès useR! .
Poster
see the publicationPollen limitation as a main driver of fruiting dynamics in oak populations
Ecology Letters . 22 ( 1 ) : 98-107
DOI: 10.1111/ele.13171
Journal article
see the publicationNew goodness-of-fit plots for censored data in the package fitdistrplus
7ème rencontres R .
Conference paper
see the publicationModelling of omics dose-response data for ecological risk assessment
Journées du GDR Ecologie Statistique (EcoStat) .
Conference paper
see the publicationPollen limitation as a main driver of fruiting dynamics in oak populations
Ecology Letters . 22 ( 1 ) : 98-107
DOI: 10.1111/ele.13171
Journal article
see the publicationDRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment
Environmental Science and Technology . 52 ( 24 ) : 14461-14468
Journal article
see the publicationMaternal reproductive senescence shapes the fitness consequences of the parental age difference in ruffed lemurs
Proceedings of the Royal Society B: Biological Sciences . 285 ( 1886 ) : 20181479
Journal article
see the publicationMareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps
Genome Biology and Evolution . 9 ( 10 ) : 2506-2509
DOI: 10.1093/gbe/evx178
Journal article
see the publicationadegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data
The R Journal . 9 ( 2 ) : 198-212
DOI: 10.32614/RJ-2017-042
Journal article
see the publicationFruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies
The American Naturalist . 188 ( 1 ) : 66-75
DOI: 10.1086/686684
Journal article
see the publicationUnknown age in health disorders: A method to account for its cumulative effect and an application to feline viruses interactions.
Epidemics . 11 : 48-55
Journal article
see the publication