Matthias Bernt

Contributions

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.

15 Tutorials

• Single Cell / Inferring single cell trajectories with Monocle3 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🧐
• Single Cell / Scanpy Parameter Iterator 🧐
• Sequence analysis / Quality Control 🧐
• Using Galaxy and Managing your Data / Group tags for complex experimental designs 🧐
• Earth Data science / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
• Earth Data science / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab 🧐
• Proteomics / Multiomics data analysis using MultiGSEA ✍️
• Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 📝 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🧐
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs ✍️
• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment ✍️ 🧐

1 Slide

• Galaxy Server administration / Galaxy Administrator Time Burden and Technology Usage 🖥

2 FAQs

• The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda?
• Where can I get planemo?

4 Video Recordings

• Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 💬 🗣
• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment 💬 🗣

4 Events

• Galaxy Training Academy 2025 🧑‍🏫
• Galaxy Training Academy 2026 🧑‍🏫
• The 2nd Galaxy Tool Development Workshop - Now Open to the wider Community! 🎪
• Galaxy Training Academy 2024 🧑‍🏫

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GitHub Activity

github Issues Reported

22 Merged Pull Requests

See all of the github Pull Requests and github Commits by Matthias Bernt.

• admin training: use miniforge
  admin
• Add missing reference to MultiGSEA tutorial
  proteomics
• Add tutorial for multigsea
  template-and-tools
  proteomics
  statistics
• Fix percentage
  microbiome
• rename Shared Data to Data
  transcriptomics
  epigenetics
  faqs
  microbiome

Reviewed 10 PRs

We love our community reviewing each other's work!

• add the SSA link to the Admin topic
  admin
  template-and-tools
  single-cell
• Add faq to force map over
  faqs
• Add DADA2 tutorial
  microbiome
• GCC21: Tool dev tutorial updates
  work-in-progress
  dev
• Fix sharing snippet
  introduction
  template-and-tools
  climate
  faqs
  single-cell

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