1 Welcome

Organisation: Data Science Platform
Responsibles: Juliana Assis (jasge@dtu.dk)
Sebastian Schulz (sebschu@dtu.dk)
Alberto Pallejà Caro (apca@dtu.dk)
Teaching Assistant: Edir Sebastian Vidal Castro (s243564@student.dtu.dk)

Welcome to the Introduction to Transcriptomics Workshop!

This workshop introduces RNA-seq data analysis, covering both the theory behind the technology and the full practical workflow — from raw reads to biological interpretation — using real E. coli data.

The course is designed for people with no or little knowledge and practical experience in transcriptomic analysis using RNA sequencing (RNAseq).

Objectives

Theory on Illumina short-read sequencing technology for transcriptome analysis
Theory and practical sessions for
- RNAseq data processing using the nf-core/rnaseq pipeline
- Statistical data analysis and visualization of RNAseq results
- Enrichment analysis — gaining biological insights from transcriptomic data
- Effective results reporting using the in-house developed software vuegen

You can also explore the DSP Transcriptomics Training repository

Time	Session
☕ 9:00 – 9:15	Welcome, coffee, and setup
🔬 9:15 – 10:00	Theory: Illumina sequencing & RNA-seq experimental design
🔄 10:00 – 10:45	Theory: nf-core/rnaseq pipeline overview
⏸️ 10:45 – 11:00	Break
💻 11:00 – 12:00	Script 01: nf-core/rnaseq — running the pipeline
🍽️ 12:00 – 13:00	Lunch
🧬 13:00 – 14:15	Script 02: Quality Control & Exploratory Data Analysis
⏸️ 14:15 – 14:30	Break
📊 14:30 – 15:30	Script 03: Differential Expression Analysis with DESeq2
⏸️ 15:30 – 15:45	Break
🔍 15:45 – 16:15	Script 04: Functional Enrichment Analysis (ORA & GSEA with mulea)
🏁 16:15 – 16:30	Wrap-up, Q&A, and closing

Material for the workshop is located at: dsp_transcriptomics_training

Below are two setup options for the practical activities:

Run the workshop in the cloud (no need to install anything).

Launch the app:

Run the workshop locally on your machine.

To run it on your own machine, install the following packages:

# Install BiocManager if needed
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

# Bioconductor packages
BiocManager::install(c(
  "DESeq2",
  "SummarizedExperiment",
  "apeglm",
  "EnhancedVolcano"
))

# CRAN packages
packages <- c(
  "dplyr",
  "ggplot2",
  "ggrepel",
  "RColorBrewer",
  "rmarkdown",
  "tidyr",
  "plotly",
  "pheatmap",
  "ggpubr",
  "here",
  "mulea"
)

install_if_missing <- function(pkg) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    install.packages(pkg, repos = "https://cloud.r-project.org/")
  } else {
    message(pkg, " already installed.")
  }
}

invisible(lapply(packages, install_if_missing))

message("All requested R packages are installed and ready to use!")

Local build of website

You need to clone the repository.

git clone https://github.com/biosustain/dsp_transcriptomics_training.git

cd dsp_transcriptomics_training

options(error = traceback)
bookdown::render_book("index.Rmd", "bookdown::gitbook")

Introduction to Transcriptomics

Workshop material

1 Welcome