Material used during the practical sessions of the BNF202 module “New technologies in the biosciences and bioinformatics pipelines” I teach at the Conservatoire national des arts et métiers.
- Package installation
Miscellaneous
Using R
- Simple data manipulation in R [ en | fr ]
- Simple algorithm in R: Training a perceptron
- Introduction to tidyverse: Manhattan plot with ggplot2
- Introduction to tidyverse: dplyr
- How to calculate the \(I\) score
Reproducible research
- Using RStudio
- Using git and GitHub in RStudio
- Using RMarkdown
Statistics
Bioinformatics
- Introduction to Bioconductor: Biostrings
- Analysing transcription start sites with BioMart
Genomics
Genotyping data
- Basic statistics with plink: the Wahlund effect
- File conversion and fixation index
- Relatedness
- A simple model to simulate genotype data
- A simple LD calculation
- Polygenic score — a toy model
Massively-parallel sequencing
- Introduction to next generation sequencing
- Introduction to IGV
- Handling massively parallel sequencing data
Transcriptomics
Databases
- FANTOM