/bfx_201909

Statistical Bioinformatics presentation

Primary LanguagePython

Presentation on statistics and bioinformatics

I gave a talk on various extensions of the linear statistical model that are used in some bioinformatics tools for analysing RNA-Seq data on 2019-09-30 to the University of Glasgow bioinformatics meetup.

If you want to look at the slides see here

If you've cloned this project and want to run it locally:

# --- project environment is managed by conda

# create build-matched environment within which to run the project
conda create --name bfx_201909 --file envs/requirements.txt

# OR
# create a less stringently-matching environment,
conda env create --name bfx_201909 --file envs/environment.yml

# ensure the environment is active
conda activate bfx_201909

# --- filepaths and project-specific stuff are setup by a tool called sidekick that is within the repo
./sidekick setup

# --- running the project is managed by snakemake
# 
# this will download all relevant data files and any images used in the presentation
# then compile the .Rmd file to an ioslides presentation
snakemake -p

You can then view the presentation (doc/stats_and_bfx.html) in the browser

When I presented this talk to the U of Glasgow bioinformatics meetup I used a xaringan presentation. The xaringan version of this talk is still available, but you'll need to pull out release v1.0.0 of the repo and save it locally.

Plan for presentation on statistics and bioinformatics

How to structure the presentation?

  • Talk or guided conversation

  • Focus on:

    • models we use everyday (and might misunderstand)

      • can we reimplement limma / edgeR from first principles

      • can we extend limma / edgeR using stan|jags / lme4 / Manova

    • novel / nonstandard techniques that lie under the hood of tools we use everyday

    • should it be "interesting new stuff" or "understanding the basics"?

What topics to include?

  • What training is provided for UoG staff / researchers

  • What is / is not covered in the MSc

  • Tools / resources to improve statistical understanding of collaborators / bioinformaticians

  • Interesting uses of stats in recent papers / projects

  • Compare some basic statistical models / methods using different tools

  • Comparative analysis of a dataset using different models

  • Local statistical reseearchers / meetups etc

What resources to highlight?

Books:

Courses (online):

Courses (UoG):

Courses (external):

Podcasts etc etc:

Who (people / groups) to mention?