
Siberchicot Aurélie
Ingénieure d'étude
UCBL
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.
- GitHub: aursiber
- ORCID: 0000-0002-7638-8318
- HAL: aurelie-siberchicot
- Google Scholar
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
- DRomics (Dose Response for Omics): CRAN -- GitHub -- shiny app -- web -- article -- IFB cloud appliance
- 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/
Organization and Program Committee
- Preditox, Training school, 2020, 2021 & 2023, Lyon (scientific committee)
- 7èmes Rencontres R, Conference, juillet 2018, Rennes (programm commitee)
- R pour le calcul, CNRS National Training Action, octobre 2015, Aussois (co-organizer)
- 2èmes Rencontres R, Conference, juin 2013, Lyon (organization committee) -- article
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 19 publications on 19 in total
PhylteR: efficient identification of outlier sequences in phylogenomic datasets
Preprint
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 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 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 publicationConference Report: Deuxièmes Rencontres R
The R Journal . 5/2 : 164--165
Journal article
see the publicationNovel measures of linkage disequilibrium that correct the bias due to population structure and relatedness
Heredity . 108 ( 3 ) : 285-291
DOI: 10.1038/hdy.2011.73
Journal article
see the publicationGenetic structure and linkage disequilibrium in 4 Vitis species
Plant and Animal Genomes Conference . : np
Conference paper
see the publicationGenetic structure and linkage disequilibrium in 4 Vitis species
Grapevine breeding and genetics .
Poster
see the publicationGenetic structure and linkage disequilibrium in four Vitis species
10. International Conference on Grapevine Breeding and Genetics .
Conference paper
see the publicationGenetic structure and linkage disequilibrium in 4 species of the Vitis genus
Génoplante .
Poster
see the publication