Authors: Saritha Kodikara
Tutors: Eva Wang
| 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 Rscript.
Click here to access the HTML workshop document.
All data used for the workshop are in data.zip.
This repository is licensed under the GNU Affero General Public License v3.0.
- The materials were inspired from the workshop r-linear-abacbs2018 from Monash Bioinformatics and QCBS R workshops from Quebec Centre for Biodiversity.