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

Introductory slides about the ABC, and who is behind the Health Data Science Sandbox and the Core Bioinformatics Facility

RStudio projects and Anaconda+Python

Conferences in the second half of 2024, introduction to Integrated Development Environments and Virtual Environments.

R analysis of bulkRNA expression matrix

Data formats and bulkRNA sequencing exercise

Introduction to bash language for bioinformatics

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…

Open coding and tutorials, single cell dimensionality reduction

Try our previous tutorials or a workshop on dimensionality reduction

Download from online databases, open coding session

Learn how to download (especially) GEO-SRA data

Practical guide to SLURM and job submissions on HPC

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

ABC: Detailed bulkRNA data alignment and quality control

Try to align a bulk dataset and perform quality control!

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

learn about seurat object structure and preprocessing of scrnaSeq data

Pixi and Desktop on genomeDK, R-clusterProfiler analysis

package-environment

clusterProfiler

pathway-analysis

Pathway enrichment analysis with R package clusterProfiler

BulkRNA deconvolution

BulkRNA deconvolution with scRNA-seq data

Single Cell Proteomics Downstream Analysis

Single Cell Proteomics

Mass Spectrometry

Data format and analysis workflow for Single Cell Proteomics in R

BulkRNA analysis on genomeDK

transcriptomics

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

GenomeDK workshops

Introductive workshop to genomeDK