Hello all! The workshop is done now. If there is any question, please contact me: baharvand79f@gmail.com Also, there is a chance to update the material or add further instructions and training files. If you want to receive an e-mail for the updates, please fill this form If you have already participated in the workshop, please let me know your feedback by filling out this form. It will help me to improve my work.
Welcome to the R workshop! Below you'll find prerequisites for the classes. This file and the repository will be updated before each session. The workshop will be a code-along and in-person workshop, and you do not need any prior knowledge of R. After each session, please fill out the feedback form.
Introduction to R
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What is R and R Studio
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Variables and missing values
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Operators
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Functions
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Conditional statements
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Data structures
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Read and write files
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Data wrangling
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Install R-4.2.1:
You can download R from these links:
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Install RStudio 2022.07.1:
You can download RStudio from this link:
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Install "tidyverse", "readr", and "dplyr" packages:
Open RStudio and click on the Packages tab in the panel. You can install them by writing their names in the new window.
Bulk RNA-seq Data Analysis with the DESeq2 Package
- how does a count table look like
- how to perform differential expression analysis
- how to visualize your results
Install tidyverse, EnhancedVolcano, ggrepel, pheatmap, RColorBrewer, d3heatmap, htmlwidgets, BiocManager, and DESeq2 packages. Run this chunk of code for this purpose. install.packages('tidyverse') install.packages('ggrepel') install.packages('pheatmap') install.packages('RColorBrewer') install.packages('htmlwidgets') install.packages('BiocManager') BiocManager::install('EnhancedVolcano') BiocManager::install("DESeq2") install.packages('devtools') devtools::install_github('talgalili/d3heatmap')
Pathway Analysis in R
- what is pathway analysis, and what are the different types
- how to perform GSEA
- how to perform ORA
- how to visualize your results
Intstall AnnotationDbi, org.Mm.eg.db, clusterProfiler, enrichplot, europepmc, and ggridges packages. Run this chunk of code for this purpose. BiocManager::install("AnnotationDbi") BiocManager::install("org.Mm.eg.db") BiocManager::install("clusterProfiler") BiocManager::install("enrichplot") install.packages("europepmc") install.packages(" ggridges")
- 08/24/2022: README file added
- 08/29/2022: Session 1 completed
- 08/30/2022: Session 2 completed
- 08/31/2022: Session 3 completed
- 09/04/2022: Files are updated