Microbial Community Analysis

Bioinformatic tools

Author

Affiliation

Corentin Maslard, PhD

UniNE

Abstract

Resume of the course

Preface

Contributors: Corentin Maslard, postdoctoral researcher in Joop E.M Vermeer lab team

Advisor:Thomas Badet

This course is an extension of my research work carried out in the EcoLeg team, under the supervision of Marion Prudent with several publications directly related to this subject, presented below:

• Maslard et al. (2021)
• Maslard et al. (2024)

This course is based on part of my thesis work

The complete repository of the project (documentation, data, script, etc.) will be available shortly at this link: https://github.com/cmaslard/phd_soybean_2021_2024/ and the overall project is presented here

Please feel free to contact me for:

• Internship
• Information
• Help with your future analyses

More informations about my work :

• Personal website
• Email
• Github
• Linkedin

• ORCID
• ResearchGate
• Google Scholar

• X (Twitter)
• HAL
• CV

Getting started

This is the third session of the bioinformatics tools course

• All resources: GitHub/tbadet
  
• Code: here
• Presentation: The presentation will be available here at the end of the course
• 3-hour course → intro, data cleaning, analysis, and formatting

No grading - just listen, follow, and ask questions!

Licence

This document is made available under the terms of the Licence Creative Commons Attribution - Non Commercial Use - Share Alike 4.0 International.

Package used in this quarto document

library(renv) # install.packages("renv")
library(dplyr)

deps <- renv::dependencies(path = ".", progress = F, quiet = T)

unique_packages <- unique(deps$Package)
writeLines(unique_packages, here::here("src/packages_use_in_this_quarto.txt"))

data.frame(
  Package = unique_packages,
  Version = sapply(unique_packages, function(pkg) {
    tryCatch(as.character(packageVersion(pkg)), error = function(e) NA)
  }),
  stringsAsFactors = FALSE
) %>% 
  #knitr::kable(caption = "List of packages used in this document", row.names = FALSE)
  DT::datatable(.,
  filter = "top",
  class = 'cell-border stripe',
  rownames = FALSE
)

Maslard, Corentin, Mustapha Arkoun, Fanny Leroy, Sylvie Girodet, Christophe Salon, and Marion Prudent. 2024. “Decoding the Double Stress Puzzle: Investigating Nutrient Uptake Efficiency and Root Architecture in Soybean Under Heat‐ and Water‐stresses.”

Maslard, Corentin, Mustapha Arkoun, Christophe Salon, and Marion Prudent. 2021. “Root Architecture Characterization in Relation to Biomass Allocation and Biological Nitrogen Fixation in a Collection of European Soybean Genotypes.” OCL 28: 48. https://doi.org/10.1051/ocl/2021033.