Siberchicot Aurélie
Ingénieure de recherche
UCBL
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
- Scientific Research Engineer (Ingénieure de Recherche) since 2023
- Scientific Project Engineer (Ingénieure d'Études) from 2012 to 2023
- Representative of the LBBE IT Department, since 2018
- ITA / BIATSS representative on the UMR council, since 2017
- Networks and IDs
- GitHub : aursiber
- ORCID : 0000-0002-7638-8318
- HAL : aurelie-siberchicot
- Google Scholar
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
- DRomics (Dose Response for Omics) : CRAN -- GitHub -- shiny app 1 -- shiny app 2 -- web -- article -- IFB cloud appliance 1 -- IFB cloud appliance 2
- kissDE (Retrieves Condition-Specific Variants in RNA-Seq Data) : Bioconductor -- GitHub
- LDcorSV (Linkage Disequilibrium Corrected by the Structure and the Relatedness) : CRAN -- article
- 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
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
- shiny server: http://lbbe-shiny.univ-lyon1.fr
- website of Statistics in Biology: http://pbil.univ-lyon1.fr/R/
Professional networks and conferences
- 3e Journées Nationales du Réseau de la Recherche Reproductible, Lyon (organization committee)
- Rencontres R (steering committee)
- 7e Rencontres R, Conference, Rennes (programm commitee)
- R pour le calcul, Action Nationale de Formation CNRS, Aussois (organization committee)
- 2e Rencontres R, Conference, Lyon (organization committee) -- article
Trainings and Courses
- UE IT bases, M1 Biodiversité, Écologie et Évolution, University Lyon 1
- UE Visualization of Biological Data, M2 Bio-informatique, University Lyon 1
- Reproducible Research in Computational Ecology, FRB-Cesab et Gdr Ecostat
- The basics of the R language, University Savoie Mont Blanc
- Programming with R: from the simplest to the most complex, Groupe Lyon Calcul
- Build your own package in R, ANF CNRS R pour le calcul
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 30 publications on 36 in total
fitdistrplus: 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 publicationModelling of omics dose-response data for ecological risk assessment
Journées du GDR Ecologie Statistique (EcoStat) .
Conference paper
see the publicationNew goodness-of-fit plots for censored data in the package fitdistrplus
7ème rencontres R .
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 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 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 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 publicationDetermining the instar of a weevil larva (Coleoptera: Curculionidae) using a parsimonious method
European Journal of Entomology . 111 ( 4 ) : 567-573
Journal article
see the publication