🧬 DSP Transcriptomics Training

Course materials are live — and we're still polishing a few things for this year!

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📚 Course Materials

All materials, resources, and a draft agenda for the day are available in this repository. We are actively updating and revising content ahead of the course.

👉 View the full repository →

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📋 Course Details

📍 Location	Room 011 / ALC2, Building 208
🕘 Duration	9:00 – 16:30
☕ Catering	Lunch & coffee provided!

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🗓️ Agenda

A draft agenda is already available in the repository. Check back closer to the date for the final version.

Time	Session
☕ 9:00 – 9:15	Welcome, coffee, and setup
🔬 9:15 – 10:00	Theory: Illumina sequencing & RNA-seq
🔄 10:00 – 10:30	Theory: nf-core/rnaseq pipeline overview
⏸️ 10:30 – 10:45	Break
💻 10:45 – 12:15	Script 01: nf-core/rnaseq — running the pipeline
	Theory: RNAseq data analysis
🍽️ 12:15 – 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

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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).

⚠️ Warning: Change the configuration at the Machine type: increase it to 4-core .

Launch the app:

Run the workshop locally on your machine.

⚠️ Warning: Please, contact me if you need help! Juliana Assis(jasge@dtu.dk)

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

# ============================================================
# DSP Transcriptomics Workshop – Package Installation Script
# ============================================================
# Run this script ONCE before the workshop to install all
# required R packages. Works on macOS, Linux, and Windows.
# Tested with R >= 4.3.
# ============================================================

## ---- 0. Helper: install only if missing --------------------

install_if_missing <- function(pkg, installer, ...) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    message("Installing: ", pkg)
    installer(pkg, ...)
  } else {
    message("Already installed: ", pkg)
  }
}

## ---- 1. CRAN packages --------------------------------------

cran_pkgs <- c(
  "tidyverse",
  "reshape2",
  "RColorBrewer",
  "pheatmap",
  "factoextra",
  "knitr",
  "kableExtra",
  "DT",
  "plotly",
  "ggpubr",
  "remotes"      # needed for GitHub installs below
)

for (pkg in cran_pkgs) {
  install_if_missing(pkg, install.packages,
                     dependencies = TRUE)
}

## ---- 2. Bioconductor packages ------------------------------

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
# Pin to the release that matches R 4.4; BiocManager picks the right
# version automatically, but you can force with: BiocManager::install(version = "3.19")

bioc_pkgs <- c(
  "DESeq2",
  "apeglm",       # recommended shrinkage estimator used with DESeq2
  "fgsea",
  "KEGGREST",
  "EnhancedVolcano"
)

for (pkg in bioc_pkgs) {
  install_if_missing(pkg, BiocManager::install,
                     update = FALSE, ask = FALSE)
}

## ---- 3. GitHub packages ------------------------------------

# mulea is not on CRAN/Bioconductor yet
if (!requireNamespace("mulea", quietly = TRUE)) {
  message("Installing mulea from GitHub (ELTEbioinformatics/mulea)")
  remotes::install_github("ELTEbioinformatics/mulea")
} else {
  message("Already installed: mulea")
}

## ---- 4. Verification ---------------------------------------

all_pkgs <- c(
  cran_pkgs,
  bioc_pkgs,
  "mulea"
)
# remove helper-only packages from the check list
check_pkgs <- setdiff(all_pkgs, "remotes")

cat("\n========== Installation check ==========\n")
ok  <- character(0)
nok <- character(0)

for (pkg in check_pkgs) {
  if (requireNamespace(pkg, quietly = TRUE)) {
    ok <- c(ok, pkg)
  } else {
    nok <- c(nok, pkg)
  }
}

cat("OK  (", length(ok),  "):", paste(ok,  collapse = ", "), "\n\n")

if (length(nok) > 0) {
  cat("FAILED (", length(nok), "):", paste(nok, collapse = ", "), "\n")
  cat("Please re-run the script or install the above packages manually.\n")
} else {
  cat("All packages installed successfully. You are ready for the workshop!\n")
}
cat("=========================================\n")

💬 See You There!

We're looking forward to seeing everyone. If you have questions before the course, feel free to reach out.

Best wishes,
The DSP Transcriptomics Training Team

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