Documentation

While it is always worth remembering an event which offers free cake (especially when it recurs with a frequency like the ABC, as you could read here), you might want to read again what has been done and said after the sugar levels drop down.

Our tutorials and instructions are self contained, thus useful for anyone, also people not attending a session.

Install R+Rstudio, first R coding problems/solutions
R
RStudio
Dataframe
Introductory slides about the ABC, and who is behind the Health Data Science Sandbox and the Core Bioinformatics Facility
Jun 13, 2024

RStudio projects and Anaconda+Python
R
RStudio
Anaconda
Python
environments
Conferences in the second half of 2024, introduction to Integrated Development Environments and Virtual Environments.
Jun 27, 2024

R analysis of bulkRNA expression matrix
R
bulkRNA
Data formats and bulkRNA sequencing exercise
Aug 20, 2024

Introduction to bash language for bioinformatics
bash
command line
The difficulty of learning bash is often underestimated by others, who expect people approaching bioinformatics to learn it automatically. Here we try to put together the…
Sep 3, 2024

Open coding and tutorials, single cell dimensionality reduction
scanpy
projection
PCA
UMAP

Try our previous tutorials or a workshop on dimensionality reduction

Sep 19, 2024

Download from online databases, open coding session
GEO
SRA
Download

Learn how to download (especially) GEO-SRA data

Oct 3, 2024

Practical guide to SLURM and job submissions on HPC
Slurm
Jobs
HPC

Learn how to create jobs on HPC and troubleshoot bugs/problems

Oct 24, 2024

Graphical applications on GenomeDK
Jupyterlab
Rstudio
LLM
GenomeDK

Learn how to launch graphical applications on GenomeDK and to integrate an LLM chatbot in Jupyterlab

Nov 28, 2024

ABC: Detailed bulkRNA data alignment and quality control
bulkRNA
alignment
QC
STAR

Try to align a bulk dataset and perform quality control!

Dec 12, 2024

Ollama for LLMs on your laptop, Introduction to Seurat, and scRNA-seq preprocessing
scrna
seurat
R

learn about seurat object structure and preprocessing of scrnaSeq data

Jan 16, 2025

Pixi and Desktop on genomeDK, R-clusterProfiler analysis
GenomeDK
pixi
conda
package-environment
R
clusterProfiler
pathway-analysis

Pathway enrichment analysis with R package clusterProfiler

Jan 30, 2025

BulkRNA deconvolution
Deconvolution
omnideconv
scRNA-seq
bulkRNA-seq

BulkRNA deconvolution with scRNA-seq data

Feb 27, 2025

Single Cell Proteomics Downstream Analysis
Single Cell Proteomics
SCP
Mass Spectrometry
QFeatures
Data Formats

Data format and analysis workflow for Single Cell Proteomics in R

Mar 13, 2025

BulkRNA analysis on genomeDK
bulkRNA
genomedk
transcriptomics

Running a bulkRNA analysis on genomeDK with a complete description on environment creation, data import, quality control

Mar 27, 2025

OMICS workshop I
R
tidyverse
omics
workshop

First omics workshop laying the foundation of R and tidyverse for the analysis of omics data. We will cover the basics of R and tidyverse which come in handy for all omics…

Feb 26, 2026

OMICS workshop II
R
tidyverse
RNA
bash
alignment
visualization

Second omics workshop building on the foundation of R and tidyverse for the analysis of omics data. We will cover preprocessing and downstream analysis topics.

Mar 26, 2026

Import and plot data in R
R
tidyverse
ggplot

Young DANDRITE association introduction workshop to R and ggplot

Apr 13, 2026

OMICS workshop III
scRNA-seq
omics
workshop

Third omics workshop building on the foundation of R and tidyverse for the analysis of omics data. We will cover preprocessing and downstream analysis topics.

Apr 23, 2026

GenomeDK workshops
GenomeDK
bash

Introductive workshop to genomeDK
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