Tutorials

MixOmics Workshop by Sebastien DEJEAN (08/09/2023)

Sebastien DEJEAN is a research engineer in the mathematical department at the University of Toulouse, France. He is specialised in statistical models and involved in the creation of the MixOmics R package. He has created the presentation and associated R script presented below. Sebastien DEJEAN has agreed that the video and documents are made available to the public domain. We wish to thank Sebastien for supporting our team with his advice and expertise - THANK YOU.

Theoretical Presentation (download presentation):

Practical Presentation (download R script):

This page will provide links to cool R code tutorials

Intro course (by Dr. Remy VILLETTE)

minimalR (by Pr. Pat Schloss, author of Mothur)

ggplot cheatsheet

ggplot animation + 3D + support accumulation

Steven Ge lab: Rtutor.ai (ChatGPT for R), ShinyGO (Gene set enrichment analysis) and iDEP (RNA-seq analysis)

Circos Plot

The following documents will allow you to acquire fundamental knowledge about flow cytometry technology (English version or French Version).

dbBact tutorielle - Amnon AMIR & Noam SHENTAL (slides, sample data)

dbBact is a tool that can associate microbiota or individual ASVs with a database of other studies and identify metadata features that may be relevant for your own study. Several types of output, including "word clouds".

ChatGPT and OpenAI - Martin LARSEN (Slides)

Of note, since my video presentation I have added more slides (you can download above).

1) Engineering - Arduino (virtual circuit design - tinkercad)

2) Engineering - 3D print (openscad software)

3) Shiny App (download final script - try the application)

4) ChatGPT detection tool.

A ChatGPT detection tool exist (GPT-2 Output Detector). Probably many more will arrive over time. I tried the tool and it works well for texts completely generated by ChatGPT, but if you ask it to improve a text not written by ChatGPT, it doesn't seem to be able to detect the improvements. Generally, it seems to work best with long texts. In conclusion, the tool works but does suffer from a significant number of false positives and false negatives. I'm not convinced that a teacher has the time to verify all texts and hand written text (copied from ChatGPT) would be difficult to test. Contrarily, one could imagine that ChatGPT would one day be able to correct our students work (that would take away a heavy evaluation burden from teachers and allow them to spend more time on their primary mission - to teach).

Copyright: Interestingly, what derives from ChatGPT is owned by the one that asked the question resulting in the production. Therefore you own the copyright to the material you produce with ChatGPT (link to OpenAI's website).

Can I use output from ChatGPT for commercial uses?
- Subject to the Content Policy and Terms, you own the output you create with ChatGPT, including the right to reprint, sell, and merchandise – regardless of whether output was generated through a free or paid plan.

Steven Gee has a website with various examples of how to use ChatGPT for bioinformatics projects.

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