Pavankumar Videm

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Former Affiliations

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.

5 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: Single Cell
• Learning Pathway: Applying single-cell RNA-seq analysis
• Learning Pathway: Epigenetics data analysis with Galaxy
• Learning Pathway: Introduction to Galaxy and Single Cell RNA Sequence analysis
• Learning Pathway: Applying single-cell RNA-seq analysis in Coding Environments

68 Tutorials

• Epigenetics / DNA Methylation data analysis 📝
• Epigenetics / Formation of the Super-Structures on the Inactive X ✍️ 🧐
• Epigenetics / CUT&RUN data analysis ✍️ 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Proteomics / Single Cell Proteomics data analysis with bioconductor-scp 📝 🧐
• Proteomics / MaxQuant and MSstats for the analysis of label-free data 🧐
• Proteomics / Metaproteomics tutorial 🧐
• Single Cell / Converting NCBI Data to the AnnData Format 📝 ⚙️ 🧐
• Single Cell / Inferring single cell trajectories with Scanpy 📝 🧐
• Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution 🧐
• Single Cell / Converting between common single cell data formats ⚙️ 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🖥 🧐
• Single Cell / Single-cell quality control with scater ⚙️
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝 🧐
• Single Cell / Analysis of plant scRNA-Seq Data with Scanpy ✍️
• Single Cell / Generating a single cell matrix using Alevin 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 🧐
• Single Cell / Inferring single cell trajectories with Scanpy (Python) 🧐
• Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets ✍️ 🧐
• Single Cell / Clustering 3K PBMCs with Seurat 📝 🧐
• Single Cell / Clustering 3K PBMCs with Scanpy ✍️ 🧐
• Single Cell / Downstream Single-cell RNA analysis with RaceID ⚙️
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat 📝 🧐
• Single Cell / Pseudobulk Analysis with Decoupler and EdgeR 📝 🧐
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets ✍️ 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝 🧐
• Single Cell / Importing files from public atlases 🧐
• Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 📝 ⚙️ 🧐
• Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) 📝 ⚙️ 🧐
• Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution 🧐
• Single Cell / Removing the effects of the cell cycle ⚙️
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) 🧐
• Single Cell / Combining single cell datasets after pre-processing 🧐
• Statistics and machine learning / Unsupervised Analysis of Bone Marrow Cells with Flexynesis 🧐
• Imaging / Content Tracking and Verification in Galaxy Workflows with ISCC-SUM 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
• Transcriptomics / Genome-wide alternative splicing analysis 📝 🧐
• Transcriptomics / RNA-RNA interactome data analysis ✍️
• Transcriptomics / Small Non-coding RNA Clustering using BlockClust ✍️ 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐
• Transcriptomics / Referenzbasierte RNA-Seq-Datenanalyse ✍️
• Transcriptomics / Análisis de datos RNA-Seq basados en referencias ✍️
• Ecology / Production d'indicateurs champs de bloc 🧐
• Transcriptomics / Analisi dei dati RNA-Seq basata su riferimenti ✍️

3 Slides

• Single Cell / Single-cell Formats and Resources 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐

2 FAQs

• Creating a dataset collection
• Creating a paired collection

4 Video Recordings

• Single Cell / Clustering 3K PBMCs with Scanpy 💬 🗣
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets 💬 🗣

10 Events

• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• A practical introduction to bioinformatics and RNA-seq using Galaxy 🧑‍🏫
• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• Galaxy Training Academy 2025 🧑‍🏫
• From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy 🧑‍🏫
• From data to discovery - Galaxy workshop at University of Graz 🧑‍🏫
• LOVE DATA week with intro to Galaxy & GTN 🎪
• Galaxy Training Academy 2026 🧑‍🏫
• BioFAIR Data to Discovery: Single-Cell Analysis with Galaxy 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

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GitHub Activity

github Issues Reported

61 Merged Pull Requests

See all of the github Pull Requests and github Commits by Pavankumar Videm.

• Add link to Single Cell track in event details
  template-and-tools
• add GTA 2026 single-cell track
  template-and-tools
• New code owners for single-cell topic
  template-and-tools
• Update CONTRIBUTORS.yaml
  template-and-tools
• Sfb992 unification
  template-and-tools
  epigenetics

Reviewed 44 PRs

We love our community reviewing each other's work!

• Revise machine learning module description
  template-and-tools
  GTA
• Add automated cell type annotation with CellTypist to Clustering 3K PBMCs with Scanpy tutorial and Vitessce visalization
  single-cell
• Create a new tutorial on the ISCC-SUM suite
  template-and-tools
  imaging
• added workshop in Graz
  template-and-tools
• MaxQuant and MSstats for the analysis of label-free data - update maxquant version and results
  proteomics

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