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 20 publications on 20 in total