Workshops

Those workshops are intended for wet lab scientists who would like to learn about bioinformatics. They are held online on 1:1 or in small groups on flexible dates.

Topics/levels can be adapted, depending on your need. Please contact me for any R / NGS data analysis workshop request.

R / RStudio

For beginners

Get comfortable using R and RStudio while analysing a dataset, from start to finish.

Learn how to get started with R, load libraries, read in tabular data, generate and modify R objects, manipulate datasets and visualize the results with ggplot.

Is this workshop for you?

This workshop is intended for researchers/PhD students in biosciences who are not comfortable using R to analyse their own data. You will learn the bascis needed to start with data analysis, including NGS. There is no prerequisites in R or genomics.

Program: (three ~2-hour sessions on three consecutive days)

  • DAY 1
    • Presentation of R and RStudio and application examples
    • Creation and manipulation of objects (variables and vectors)
    • Logical subsetting
    • Built-in functions
  • DAY 2
    • Creation of lists and application example (Venn diagrams)
    • Introduction to the example dataset (vcf format)
    • R packages presentation
  • DAY 3
    • Creation and manipulation of data frames
    • ggplot2 application examples (live coding session)


Next available session: May 2025

from 10 am to ~12.15 pm (GMT+2 Central Europe)

from 12 pm to ~2.15 pm (GMT+3 Arabia Standard Time)

from 5 pm to ~7.15 pm (GMT+8 Singapore)


Intermediate Level

Improve your R scripts:

  • use conditional statements (perform different actions based on different conditions)

  • implement your own functions (reuse code that performs a specific task)

  • efficiently manipulate vectors (repetitively perform an action without using loops)

  • customize your plots (advanced ggplot2)

  • more on request

Next available session: On demand


rmarkdown (Intermediate)

Learn how to generate professional and interactive html reports using R:

  • automate report generation
    • open output files and extract results
    • generate a quick data overview
  • static and interactive plots
    • select category, zoom-in/out, show annotations
  • interactive tables
    • sort by colomn, search fonction

Next available session: On demand

Shiny (Advanced - coming soon)

Implement your own Shiny app, and allow your collaborators to explore and visualize your datasets easily.



Made in R by Clem M

ABN 62 778 900 494

Email:

Linux / MacOS command line


Why learn command line / batch script?

Most bioinformatics tools run on Linux systems using command lines. Workflows and runs can be automated using batch scripting.

For beginners

  • connect to a Linux server
  • understand the file hierarchy structure
    • manipulate files/directories
  • write basic bash scripts
    • learn about variables, loops and conditional statements
  • implement automated tasks

Made in R by Clem M

ABN 62 778 900 494

Email:

NGS data Analysis


Most NGS data analysis start after sequencing, with fastq files. The data are usually first analysed on Linux systems and downstream analysis can then be processed with specialised R packages.


RNAseq / DNAseq Analysis

  • Pre-process raw data
  • do QC analysis
  • align your reads to a reference genome
  • do basic downstream analysis:
    • Differential Gene Expression
    • SNP calling

Next available session: On demand



Made in R by Clem M

ABN 62 778 900 494

Email:

Testimonials

I always appreciate student’s feedback and suggestions to improve my content.

Feedback from previous workshops


“Thanks Clem that was super helpful” (R for beginners workshop)

“Great workshop” (R for beginners workshop)

“That’s perfect” (R for beginners workshop)

“Excellent all throughout” (R for beginners workshop)

“Keep organising follow up workshop similar to this” (R for beginners workshop)

“Keep organising and helping researchers” (R for beginners workshop)

“I feel it was run really well” (R for beginners workshop)



Made in R by Clem M

ABN 62 778 900 494

Email:

About me

After a Master in Bioinformatics obtained in 2012 (Bordeaux - France), I worked as a bioinformatics research assistant in molecular biology (ZMBH, Heidelberg - Germany) and medical research (dkfz, Heidelberg - Germany) for 4 years.

I then obtained a PhD in Applied Bioinformatics (UWA, Perth - Australia in collaboration with BASF, Ghent - Belgium), focused on NGS analysis and epigenetics, in 2021.


Since then, I work as a bioinformatician in one of the main Australian sequencing facilities. In parallel, I became a consultant in web development and started implementing web apps (in Shiny R) for a civil engineering company (Engineering Design and Certifications, Gold Coast - Australia) specialized in structural engineering.



In order to offer the best support in helping people perform their own data analysis independently, I became a Carpentries Instructor in 2023. The Carpentries Instructor Training curriculum was originally released in 2016 and is focused on evidence-based teaching practices.

I have a specific interest for data visualization and generation of user-friendly interfaces which help scientists get a clear overview of every project outcome.



Made in R by Clem M

ABN 62 778 900 494

Email:

Contact

For any request, please contact me at:



Made in R by Clem M

ABN 62 778 900 494

Email: