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.

ABC.1: Install R+Rstudio, first R coding problems/solutions

Things worth remembering from the ABC.1

ABC.2: RStudio projects and Anaconda+Python

Things worth remembering from the ABC.2

ABC.3: R analysis of bulkRNA expression matrix

Things worth remembering from the ABC.3

ABC.4: Introduction to bash language for bioinformatics

Slides and bash intro at the ABC.4

ABC.5: open coding and tutorials, single cell dimensionality reduction

ABC.5: try our previous tutorials or a workshop on dimensionality reduction

ABC.6: Download from online databases, open coding session

Learn how to download (especially) GEO-SRA data

Workshop: Use GenomeDK

Introductive workshop to genomeDK

ABC.7: Practical guide to SLURM and job submissions on HPC

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

ABC.9: Graphical applications on GenomeDK

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

ABC.10: Detailed bulkRNA data alignment and quality control

Try to align a bulk dataset and perform quality control!

ABC.11: Ollama for LLMs on your laptop, Introduction to Seurat, and scRNA-seq preprocessing

learn about seurat object structure and preprocessing of scrnaSeq data

ABC.12: Pixi and Desktop on genomeDK, R-clusterProfiler analysis

package-environment

clusterProfiler

pathway-analysis

Pathway enrichment analysis with R package clusterProfiler

ABC.13: BulkRNA deconvolution

BulkRNA deconvolution with scRNA-seq data

ABC.14: Single Cell Proteomics Downstream Analysis

Single Cell Proteomics

Mass Spectrometry

Data format and analysis workflow for Single Cell Proteomics in R

ABC.15: bulkRNA analysis on genomeDK

transcriptomics

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