Authors: Saritha Kodikara
Tutors: Ilariya Tarasova, Yidi Deng
| Audience | Prerequisites | Duration |
|---|---|---|
| Biologists | Intro to R | ~ 2.5 hours |
This repository includes material for our workshop 'Linear models'. This workshop will introduce the fundamental principles of linear models and linear mixed effect models, with hands-on applications for the analysis of gene expression data, using base and limma R packages.
Install R first, then RStudio. Download the most recent version of R and RStudio using the links below:
Install the R packages. Type the R command lines:
# Install tidyverse package using CRAN
install.packages(c("tidyverse", "nlme", "ggpubr", "MuMIn"))
# Install edgeR and limma packages using BiocManager
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install(c("edgeR","limma"))
# Test if packages have been installed
library(tidyverse) # working with data frames, plotting
library(edgeR) # cpm, etc -- RNA-Seq normalization
library(limma) # lmFit, etc -- fitting many models
library(nlme) # lme
library(ggpubr) # ggqqplot
library(MuMIn) # AICc
Click here to access the slides.
Click here to access the HTML workshop document.
All data used for the workshop are in data.zip.
- The materials were inspired from the workshop r-linear-abacbs2018 from Monash Bioinformatics and QCBS R workshops from Quebec Centre for Biodiversity.