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
  • Potenchêne program (Gip ECOFOR, BGF) -- article
  • AGEX program (ANR-15-CE32-0002-01)  -- article
  • CoCoReCo program (ANR JC09-470585) -- article
  • website of Statistics in Biology: http://pbil.univ-lyon1.fr/R/

Ecotoxicology

Genetics and Genomics

  • 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
  • Mondrian (A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events): CRAN -- GitHub -- shiny app

Mathematical Statistics

  • fitdistrplus (Help to Fit of a Parametric Distribution to Non-Censored or Censored Data): CRAN -- web

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 INRA (2019) AI BAP E Assistant.e statisticien.ne
  • Concours externe INRA (2019) IE BAP E Administrateur.trice des systèmes d’information
  • Concours externe CNRS (2017) IE BAP E Développement et déploiement d’applications

Supervision

  • 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 17 publications on 17 in total