Björn Grüning
Affiliations
EuroScienceGateway
EOSC-Life
BeYond-COVID
de.NBI
CRC992
ELIXIR-CONVERGE
UFR
ELIXIR EuropeContributions
The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.
Editorial Roles
This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.
- Topic: Galaxy Server administration
- Topic: Computational chemistry
- Topic: Contributing to the Galaxy Training Material
- Topic: Proteomics
- Topic: Variant Analysis
Tutorials
- Using Galaxy and Managing your Data / RStudio in Galaxy 🧐
- Using Galaxy and Managing your Data / Getting started with Onedata distributed storage 🧐
- Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy 🧐
- Using Galaxy and Managing your Data / Group tags for complex experimental designs 🧐
- Using Galaxy and Managing your Data / Downloading and Deleting Data in Galaxy 🧐
- Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line 🧐
- Using Galaxy and Managing your Data / JupyterLab in Galaxy 🧐
- Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows 🧐
- Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis 🧐
- Using Galaxy and Managing your Data / Exporting to Onedata remote 🧐
- Using Galaxy and Managing your Data / Understanding Galaxy history system 📝 🧐
- Using Galaxy and Managing your Data / Extracting Workflows from Histories 🧐
- Using Galaxy and Managing your Data / Importing (uploading) data from Onedata 🧐
- Using Galaxy and Managing your Data / Using Workflow Parameters 🧐
- Using Galaxy and Managing your Data / Name tags for following complex histories 🧐
- Using Galaxy and Managing your Data / Creating high resolution images of Galaxy Workflows 🧐
- Using Galaxy and Managing your Data / Using dataset collections 🧐
- Using Galaxy and Managing your Data / Rule Based Uploader: Advanced 🧐
- Using Galaxy and Managing your Data / Onedata user-owned storage 🧐
- Using Galaxy and Managing your Data / Submitting sequence data to ENA 🧐
- Visualisation / Visualisation with Circos 🧐
- Visualisation / Genomic Data Visualisation with JBrowse 🧐
- Visualisation / Ploting a Microbial Genome with Circos 🧐
- Galaxy Server administration / Customizing the look of Galaxy (Manual) 🧐
- Galaxy Server administration / Galaxy Database schema ✍️ 🧐
- Galaxy Server administration / Galaxy Tool Management with Ephemeris 🧐
- Galaxy Server administration / Mapping Jobs to Destinations using TPV ✍️ 🧐
- Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
- Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
- Galaxy Server administration / Customizing the look of Galaxy 🧐
- Galaxy Server administration / Galaxy Installation on Kubernetes 🧐
- Galaxy Server administration / Ansible 🧐
- Galaxy Server administration / Create a subdomain for your community on UseGalaxy.eu 🧐
- Galaxy Server administration / Setting up Celery Workers for Galaxy 🧐
- Galaxy Server administration / Data Libraries 🧐
- Galaxy Server administration / Reference Data with CVMFS without Ansible 🧐
- Galaxy Server administration / Automation with Jenkins 🧐
- Galaxy Server administration / Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD) 🧐
- Galaxy Server administration / External Authentication 🧐
- Galaxy Server administration / Galaxy Interactive Tools 🧐
- Galaxy Server administration / Managing Galaxy on Kubernetes 🧐
- Galaxy Server administration / Deploying a compute cluster in OpenStack via Terraform 🧐
- Galaxy Server administration / Reference Data with CVMFS 🧐
- Galaxy Server administration / Upgrading Galaxy 🧐
- Galaxy Server administration / Connecting Galaxy to a compute cluster ✍️ 🧐
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
- Galaxy Server administration / Adding file-sources to Galaxy 🧐
- Galaxy Server administration / Distributed Object Storage 🧐
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
- Galaxy Server administration / Galaxy Installation with Ansible 🧐
- Galaxy Server administration / Galaxy Monitoring with Reports ✍️ 🧐
- Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
- Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
- Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab 🧐
- Climate / Analyse Argo data 🧐
- Climate / Visualize Climate data with Panoply netCDF viewer 🧐
- Climate / Ocean Data View (ODV) 🧐
- Climate / Getting your hands-on climate data 🧐
- Climate / Ocean's variables study 🧐
- Climate / Collaboration with JupyterGIS 🧐
- Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) ✍️ 🧐
- Proteomics / Machine Learning Modeling of Anticancer Peptides 🧐
- Proteomics / Statistical analysis of DIA data 🧐
- Proteomics / Peptide Library Data Analysis 🧐
- Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker ✍️ 🧐
- Proteomics / Proteogenomics 1: Database Creation 🧐
- Proteomics / Annotating a protein list identified by LC-MS/MS experiments 🧐
- Proteomics / Secretome Prediction ✍️ 🧐
- Proteomics / Clinical Metaproteomics 4: Quantitation 🧐
- Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS ✍️ 🧐
- Proteomics / MaxQuant and MSstats for the analysis of label-free data 🧐
- Proteomics / Protein FASTA Database Handling ✍️ 🧐
- Proteomics / Peptide and Protein ID using OpenMS tools ✍️ 🧐
- Proteomics / Mass spectrometry imaging: Loading and exploring MSI data ✍️ 🧐
- Proteomics / metaQuantome 3: Taxonomy 🧐
- Proteomics / DIA Analysis using OpenSwathWorkflow 🧐
- Proteomics / Proteogenomics 3: Novel peptide analysis 🧐
- Proteomics / EncyclopeDIA 🧐
- Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method ✍️ 🧐
- Proteomics / Multiomics data analysis using MultiGSEA 🧐
- Proteomics / Clinical Metaproteomics 2: Discovery 🧐
- Proteomics / MaxQuant and MSstats for the analysis of TMT data 🧐
- Proteomics / Library Generation for DIA Analysis 🧐
- Proteomics / Clinical Metaproteomics 3: Verification 🧐
- Proteomics / Proteogenomics 2: Database Search 🧐
- Proteomics / Clinical Metaproteomics 5: Data Interpretation 🧐
- Proteomics / Metaproteomics tutorial 🧐
- Proteomics / Label-free data analysis using MaxQuant 🧐
- Proteomics / metaQuantome 1: Data creation 🧐
- Proteomics / metaQuantome 2: Function 🧐
- Proteomics / Clinical Metaproteomics 1: Database-Generation 🧐
- Microbiome / 16S Microbial Analysis with mothur (extended) 🧐
- Microbiome / Analyses of metagenomics data - The global picture 🧐
- Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data 🧐
- Microbiome / 16S Microbial analysis with Nanopore data 🧐
- Microbiome / Antibiotic resistance detection 🧐
- Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition 🧐
- Imaging / Tracking of mitochondria and capturing mitoflashes 🧐
- Imaging / Nucleoli segmentation and feature extraction using CellProfiler 🧐
- Imaging / Analyse HeLa fluorescence siRNA screen 🧐
- Imaging / Voronoi segmentation 🧐
- Imaging / Using BioImage.IO models for image analysis in Galaxy 🧐
- Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy 📝 🧐
- Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 🧐
- Imaging / Introduction to Image Analysis using Galaxy 🧐
- Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
- Introduction to Galaxy Analyses / NGS data logistics 🧐
- Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐
- Introduction to Galaxy Analyses / From peaks to genes ✍️ 🧐
- Introduction to Galaxy Analyses / A short introduction to Galaxy 🧐
- Introduction to Galaxy Analyses / Data Manipulation Olympics 🧐
- Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses 🧐
- Introduction to Galaxy Analyses / Galaxy Basics for genomics ✍️ 🧐
- Introduction to Galaxy Analyses / IGV Introduction 🧐
- Genome Annotation / Genome annotation with Prokka 🧐
- Genome Annotation / Genome annotation with Helixer 🧐
- Genome Annotation / Genome annotation with Maker 🧐
- Genome Annotation / Bacterial Genome Annotation 🧐
- Genome Annotation / Genome Annotation ✍️ 🧐
- Genome Annotation / Functional annotation of protein sequences 🧐
- Genome Annotation / Genome annotation with Funannotate 🧐
- Genome Annotation / Essential genes detection with Transposon insertion sequencing 🧐
- Genome Annotation / CRISPR screen analysis 🧐
- Genome Annotation / Masking repeats with RepeatMasker 🧐
- Genome Annotation / Genome annotation with Maker (short) 🧐
- Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) 🧐
- Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc 🧐
- Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes) 🧐
- Genome Annotation / Identification of AMR genes in an assembled bacterial genome 🧐
- Single Cell / Inferring single cell trajectories with Scanpy (Python) 🧐
- Single Cell / Pre-processing of Single-Cell RNA Data 🧐
- Single Cell / Comparing inferred cell compositions using MuSiC deconvolution 🧐
- Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets 🧐
- Single Cell / Scanpy Parameter Iterator 🧐
- Single Cell / Inferring single cell trajectories with Monocle3 🧐
- Single Cell / Inferring single cell trajectories with Scanpy 🧐
- Single Cell / Generating a single cell matrix using Alevin 🧐
- Single Cell / Inferring single cell trajectories with Monocle3 (R) 🧐
- Single Cell / Pre-processing of 10X Single-Cell RNA Datasets 🧐
- Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 📝 🧐
- Single Cell / Clustering 3K PBMCs with Seurat 🧐
- Single Cell / Converting NCBI Data to the AnnData Format 🧐
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat 🧐
- Single Cell / Analysis of plant scRNA-Seq Data with Scanpy 🧐
- Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) 🧐
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🧐
- Single Cell / Understanding Barcodes 🧐
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 🧐
- Single Cell / Single-cell quality control with scater 🧐
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) 🧐
- Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 📝 🧐
- Single Cell / Clustering 3K PBMCs with Scanpy 🧐
- Single Cell / Converting between common single cell data formats 🧐
- Single Cell / Importing files from public atlases 🧐
- Single Cell / Combining single cell datasets after pre-processing 🧐
- Single Cell / Pseudobulk Analysis with Decoupler and EdgeR 🧐
- Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution 🧐
- Single Cell / Downstream Single-cell RNA analysis with RaceID 🧐
- Single Cell / Removing the effects of the cell cycle 🧐
- Single Cell / Bulk RNA Deconvolution with MuSiC 🧐
- Development in Galaxy / Contributing to BioBlend as a developer 🧐
- Development in Galaxy / Generic plugins 🧐
- Development in Galaxy / JavaScript plugins ✍️ 🧐
- Development in Galaxy / Setting up a dev Onedata instance 🧐
- Development in Galaxy / Galaxy Webhooks ✍️ 🧐
- Development in Galaxy / Debugging Galaxy 🧐
- Development in Galaxy / Galaxy Interactive Tools 🧐
- Development in Galaxy / Data source integration 🧐
- Development in Galaxy / ToolFactory: Generating Tools From Simple Scripts 🧐
- Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters 🧐
- Evolution / Tree thinking for tuberculosis evolution and epidemiology 🧐
- Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) 🧐
- Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS 🧐
- Metabolomics / Mass spectrometry: LC-MS analysis 🧐
- Metabolomics / Mass spectrometry imaging: Finding differential analytes 🧐
- Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes 🧐
- Foundations of Data Science / A (very) brief history of genomics 🧐
- Foundations of Data Science / SQL Educational Game - Murder Mystery 🧐
- Foundations of Data Science / Data manipulation with Pandas 🧐
- Foundations of Data Science / Make & Snakemake 🧐
- Foundations of Data Science / Introduction to sequencing with Python (part one) 🧐
- Foundations of Data Science / Versioning your code and data with git 🧐
- Foundations of Data Science / Introduction to sequencing with Python (part two) 🧐
- Foundations of Data Science / Introduction to sequencing with Python (part four) 🧐
- Foundations of Data Science / Introduction to sequencing with Python (part three) 🧐
- Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) 🧐
- Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer 🧐
- Epigenetics / Formation of the Super-Structures on the Inactive X 🧐
- Epigenetics / Identification of the binding sites of the Estrogen receptor 🧐
- Epigenetics / Infinium Human Methylation BeadChip 🧐
- Epigenetics / CUT&RUN data analysis 🧐
- Epigenetics / DNA Methylation data analysis 🧐
- Epigenetics / ATAC-Seq data analysis 🧐
- Galaxy Community Building / Make your tools available on your subdomain 🧐
- Materials Science / Finding the muon stopping site with pymuon-suite in Galaxy 🧐
- FAIR Data, Workflows, and Research / Data Registration 🧐
- FAIR Data, Workflows, and Research / RO-Crate in Python 🧐
- FAIR Data, Workflows, and Research / DataPLANT ARCs 🧐
- FAIR Data, Workflows, and Research / RO-Crate - Introduction 🧐
- FAIR Data, Workflows, and Research / Persistent Identifiers 🧐
- FAIR Data, Workflows, and Research / Exporting Workflow Run RO-Crates from Galaxy 🧐
- FAIR Data, Workflows, and Research / Access 🧐
- FAIR Data, Workflows, and Research / Best practices for workflows in GitHub repositories 🧐
- FAIR Data, Workflows, and Research / Metadata 🧐
- FAIR Data, Workflows, and Research / FAIR and its Origins 🧐
- Assembly / Decontamination of a genome assembly 🧐
- Assembly / Unicycler Assembly 🧐
- Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data 🧐
- Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step 🧐
- Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads 🧐
- Assembly / Genome assembly using PacBio data 🧐
- Assembly / De Bruijn Graph Assembly 🧐
- Assembly / Making sense of a newly assembled genome 🧐
- Assembly / ERGA post-assembly QC 🧐
- Assembly / Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data 🧐
- Assembly / Assembly of the mitochondrial genome from PacBio HiFi reads 🧐
- Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) 🧐
- Assembly / Chloroplast genome assembly 🧐
- Assembly / An Introduction to Genome Assembly 🧐
- Contributing to the Galaxy Training Material / Design and plan session, course, materials 🧐
- Contributing to the Galaxy Training Material / Preview the GTN website as you edit your training material ✍️ 🧐
- Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials ✍️ 🧐
- Contributing to the Galaxy Training Material / Adding Quizzes to your Tutorial 🧐
- Contributing to the Galaxy Training Material / GTN Metadata 🧐
- Contributing to the Galaxy Training Material / FAIR-by-Design methodology 🧐
- Contributing to the Galaxy Training Material / Adding auto-generated video to your slides 🧐
- Contributing to the Galaxy Training Material / Principles of learning and how they apply to training and teaching 🧐
- Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
- Contributing to the Galaxy Training Material / Contributing with GitHub via its interface 🧐
- Contributing to the Galaxy Training Material / Contributing to the Galaxy Training Network with GitHub 🧐
- Contributing to the Galaxy Training Material / Creating content in Markdown 📝 🧐
- Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours ✍️ 🧐
- Contributing to the Galaxy Training Material / Including a new topic 🧐
- Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
- Contributing to the Galaxy Training Material / Teaching Python 🧐
- Teaching and Hosting Galaxy training / Hybrid training 🧐
- Teaching and Hosting Galaxy training / Motivation and Demotivation 🧐
- Teaching and Hosting Galaxy training / Training Infrastructure as a Service 🧐
- Teaching and Hosting Galaxy training / Set up a Galaxy for Training 🧐
- Teaching and Hosting Galaxy training / Running a workshop as instructor ✍️ 🧐
- Teaching and Hosting Galaxy training / Galaxy Admin Training 🧐
- Teaching and Hosting Galaxy training / Organizing a workshop 🧐
- Teaching and Hosting Galaxy training / Teaching online 🧐
- Teaching and Hosting Galaxy training / Training techniques to enhance learner participation and engagement 🧐
- Teaching and Hosting Galaxy training / Assessment and feedback in training and teachings 🧐
- Statistics and machine learning / Regression in Machine Learning 🧐
- Statistics and machine learning / Predicting Mutation Impact with Zero-shot Learning using a pretrained DNA LLM 🧐
- Statistics and machine learning / Introduction to deep learning 🧐
- Statistics and machine learning / Supervised Learning with Hyperdimensional Computing 🧐
- Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) 🧐
- Statistics and machine learning / Interval-Wise Testing for omics data 🧐
- Statistics and machine learning / Basics of machine learning 🧐
- Statistics and machine learning / Optimizing DNA Sequences for Biological Functions using a DNA LLM 🧐
- Statistics and machine learning / Fine-tuning a LLM for DNA Sequence Classification 🧐
- Statistics and machine learning / Age prediction using machine learning 🧐
- Statistics and machine learning / A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy 🧐
- Statistics and machine learning / Fine tune large protein model (ProtTrans) using HuggingFace 🧐
- Statistics and machine learning / Classification in Machine Learning 🧐
- Statistics and machine learning / Machine learning: classification and regression 🧐
- Statistics and machine learning / Building the LORIS LLR6 PanCancer Model Using PyCaret 🧐
- Statistics and machine learning / Generating Artificial Yeast DNA Sequences using a DNA LLM 🧐
- Statistics and machine learning / Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences 🧐
- Statistics and machine learning / Introduction to Machine Learning using R 🧐
- Statistics and machine learning / Text-mining with the SimText toolset 🧐
- Statistics and machine learning / Clustering in Machine Learning 🧐
- Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles 🧐
- Sequence analysis / NCBI BLAST+ against the MAdLand 🧐
- Sequence analysis / Quality Control 🧐
- Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data 🧐
- Sequence analysis / Mapping 🧐
- Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates 🧐
- Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP 🧐
- Variant Analysis / Microbial Variant Calling 🧐
- Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data 🧐
- Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis 🧐
- Variant Analysis / M. tuberculosis Variant Analysis 🧐
- Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC 🧐
- Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data 🧐
- Variant Analysis / Calling variants in diploid systems 🧐
- Variant Analysis / Calling variants in non-diploid systems 🧐
- Variant Analysis / Calling very rare variants 🧐
- Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease ✍️ 🧐
- Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs 🧐
- Variant Analysis / Mapping and molecular identification of phenotype-causing mutations 🧐
- Computational chemistry / High Throughput Molecular Dynamics and Analysis ✍️ 🧐
- Computational chemistry / Analysis of molecular dynamics simulations 🧐
- Computational chemistry / Setting up molecular systems 🧐
- Computational chemistry / Running molecular dynamics simulations using NAMD 🧐
- Computational chemistry / Running molecular dynamics simulations using GROMACS 🧐
- Computational chemistry / Protein-ligand docking 🧐
- Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring 🧐
- Ecology / RAD-Seq Reference-based data analysis 🧐
- Ecology / Ecoregionalization workflow tutorial 🧐
- Ecology / RAD-Seq to construct genetic maps 🧐
- Ecology / Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities 🧐
- Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite 🧐
- Ecology / QGIS Web Feature Services 🧐
- Ecology / Obis marine indicators 🧐
- Ecology / Cleaning GBIF data using OpenRefine 🧐
- Ecology / Regional GAM 🧐
- Ecology / Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS 🧐
- Ecology / From NDVI data with OpenEO to time series visualisation with Holoviews 🧐
- Ecology / Marine Omics identifying biosynthetic gene clusters 🧐
- Ecology / RAD-Seq de-novo data analysis 🧐
- Transcriptomics / Pathway analysis with the MINERVA Platform 🖥 🧐
- Transcriptomics / Genome-wide alternative splicing analysis 🧐
- Transcriptomics / RNA Seq Counts to Viz in R 🧐
- Transcriptomics / 1: RNA-Seq reads to counts 🧐
- Transcriptomics / 3: RNA-seq genes to pathways 🧐
- Transcriptomics / Reference-based RNAseq data analysis (long) 🧐
- Transcriptomics / 2: RNA-seq counts to genes 🧐
- Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection 🧐
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot 🧐
- Transcriptomics / Reference-based RNA-Seq data analysis 🧐
- Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis 🧐
- Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana 🧐
- Transcriptomics / Visualization of RNA-Seq results with heatmap2 🧐
- Transcriptomics / GO Enrichment Analysis 🧐
- Transcriptomics / Differential abundance testing of small RNAs 🧐
- Transcriptomics / RNA-RNA interactome data analysis 🧐
- Transcriptomics / RNA-Seq analysis with AskOmics Interactive Tool 🧐
- Transcriptomics / De novo transcriptome reconstruction with RNA-Seq 🧐
Slides
- Development in Galaxy / Galaxy from a developer point of view 🧐
- Materials Science / Introduction to Muon Spectroscopy 🧐
- Using Galaxy and Managing your Data / Galaxy workflows in Dockstore 🧐
- Using Galaxy and Managing your Data / Submitting SARS-CoV-2 sequences to ENA 🧐
- Visualisation / Visualisations in Galaxy 🧐
- Visualisation / Circos 🧐
- Visualisation / JBrowse 🧐
- Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration ✍️ 🧐
- Galaxy Server administration / Galaxy Tool Management with Ephemeris 🧐
- Galaxy Server administration / User, Role, Group, Quota, and Authentication managment ✍️ 🧐
- Galaxy Server administration / Galaxy from an administrator's point of view ✍️ 🧐
- Galaxy Server administration / Advanced customisation of a Galaxy instance ✍️ 🧐
- Galaxy Server administration / Galaxy Monitoring with gxadmin ✍️ 🧐
- Galaxy Server administration / Ansible 🧐
- Galaxy Server administration / Docker and Galaxy ✍️ 🧐
- Galaxy Server administration / Galaxy Monitoring ✍️ 🧐
- Galaxy Server administration / Empathy 🧐
- Galaxy Server administration / Galaxy Interactive Tools 🧐
- Galaxy Server administration / Gearing towards production 🧐
- Galaxy Server administration / Terraform 🧐
- Galaxy Server administration / Reference Data with CVMFS 🧐
- Galaxy Server administration / Connecting Galaxy to a compute cluster ✍️ 🧐
- Galaxy Server administration / uWSGI 🧐
- Galaxy Server administration / Reference Genomes in Galaxy 🧐
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana ✍️ 🧐
- Galaxy Server administration / Server: Other ✍️ 🧐
- Galaxy Server administration / Galaxy on the Cloud 🧐
- Galaxy Server administration / Galaxy Troubleshooting 🧐
- Galaxy Server administration / Storage Management 🧐
- Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
- Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 🧐
- Microbiome / Introduction to Microbiome Analysis 🧐
- Microbiome / Introduction to metatranscriptomics 🧐
-
Imaging
/
Nucleoli Segmentation
&
Feature Extraction
using CellProfiler 🧐 - Introduction to Galaxy Analyses / Options for using Galaxy 🧐
- Introduction to Galaxy Analyses / Introduction to Galaxy 🧐
- Introduction to Galaxy Analyses / A Short Introduction to Galaxy 🧐
- Genome Annotation / Genome annotation with Prokka 🧐
- Genome Annotation / Introduction to Genome Annotation 🧐
- Single Cell / Dealing with Cross-Contamination in Fixed Barcode Protocols 🧐
- Single Cell / Trajectory analysis 🧐
- Single Cell / Automated Cell Annotation 🧐
- Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 🧐
- Single Cell / Plates, Batches, and Barcodes 🧐
- Single Cell / Clustering 3K PBMCs with Scanpy 🧐
- Single Cell / Single-cell Formats and Resources 🧐
- Single Cell / An introduction to scRNA-seq data analysis 🧐
- Development in Galaxy / Generic plugins 🧐
- Development in Galaxy / Galaxy Interactive Environments ✍️ 🧐
- Development in Galaxy / Visualizations: JavaScript Plugins ✍️ 🧐
- Development in Galaxy / Galaxy Webhooks ✍️ 🧐
- Development in Galaxy / Tool Dependencies and Containers ✍️ 🧐
- Development in Galaxy / Prerequisites for building software/conda packages 🧐
- Development in Galaxy / Tool Shed: sharing Galaxy tools 🧐
- Development in Galaxy / Scripting Galaxy using the API and BioBlend 🧐
- Development in Galaxy / Tool development and integration into Galaxy ✍️ 🧐
- Development in Galaxy / Tool Dependencies and Conda ✍️ 🧐
- Development in Galaxy / Galaxy Code Architecture ✍️ 🧐
- Development in Galaxy / Galaxy Interactive Tours ✍️ 🧐
- Metabolomics / Mass spectrometry: LC-MS preprocessing - advanced 🧐
- Epigenetics / ChIP-seq data analysis 🧐
- Epigenetics / EWAS Epigenome-Wide Association Studies Introduction 🧐
- Epigenetics / Introduction to DNA Methylation data analysis 🧐
- Epigenetics / Introduction to ChIP-Seq data analysis 🧐
- Assembly / Unicycler Assembly 🧐
- Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads 🧐
- Assembly / Genome assembly and assembly QC - Introduction short version 🧐
- Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material 🧐
- Contributing to the Galaxy Training Material / Creating Slides 🧐
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line 🧐
- Teaching and Hosting Galaxy training / Overview of the Galaxy Training Material for Instructors 🧐
- Statistics and machine learning / Regression in Machine Learning 🧐
- Statistics and machine learning / Convolutional neural networks (CNN) Deep Learning - Part 3 🧐
- Statistics and machine learning / Introduction to Machine learning 🧐
- Statistics and machine learning / Fine-tuning Protein Language Model 🧐
- Statistics and machine learning / Classification in Machine Learning 🧐
- Sequence analysis / Quality Control 🧐
- Sequence analysis / Mapping 🧐
- Variant Analysis / Introduction to Variant analysis 🧐
- Transcriptomics / Identification of non-canonical ORFs and their potential biological function 🧐
- Transcriptomics / Introduction to Transcriptomics 🧐
- Single Cell / Introducción al análisis de datos de scRNA-seq 🧐
- Single Cell / Una introducción al análisis de datos scRNA-seq 🧐
FAQs
Events
- 2023 Galaxy Admin Training (Ghent) 🎪
- Galaxy Training Academy 2025 🧑🏫
- Galaxy Training Academy 2024 🧑🏫
GitHub Activity
github Issues Reported
64 Merged Pull Requests
See all of the github Pull Requests and github Commits by Björn Grüning.
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update contributors for Teresa and Lisanna
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Add ELIXIR and a few other affiliations
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Add proper tags to fit tutorials in ELIXIR topic
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