Pavankumar Videm

Affiliations

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

95 Tutorials

• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Digital Humanities / Montreal Forced Aligner 🧐
• Computational chemistry / Protein-ligand docking 🧐
• Single Cell / Pseudobulk Analysis with Decoupler and EdgeR 📝 🧐
• Single Cell / Batch Correction and Integration with Seurat or Scanpy 🧐
• Single Cell / Inferring single cell trajectories with Scanpy (Python) 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝 🧐
• Single Cell / Understanding Barcodes 🧐
• Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution 🧐
• Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution 🧐
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝 🧐
• Single Cell / Inferring single cell trajectories with Scanpy 📝 🧐
• Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution 🧐
• Single Cell / Removing the effects of the cell cycle ⚙️ 🧐
• Single Cell / Downstream Single-cell RNA analysis with RaceID ⚙️
• Single Cell / Clustering 3K PBMCs with Scanpy ✍️ 🧐
• Single Cell / Converting between common single cell data formats ⚙️ 🧐
• Single Cell / Analysis of plant scRNA-Seq Data with Scanpy ✍️ 🧐
• Single Cell / Comparing inferred cell compositions using MuSiC deconvolution 🧐
• Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 📝 ⚙️ 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 🧐
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets ✍️ 🧐
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat 📝 🧐
• Single Cell / Combining single cell datasets after pre-processing 🧐
• Single Cell / Bulk RNA Deconvolution with MuSiC 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🖥 🧐
• Single Cell / Converting NCBI Data to the AnnData Format 📝 ⚙️ 🧐
• Single Cell / Single-cell quality control with scater ⚙️
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) 🧐
• Single Cell / Importing files from public atlases 🧐
• Single Cell / Clustering 3K PBMCs with Seurat 📝 🧐
• Single Cell / Generating a single cell matrix using Alevin 🧐
• Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets ✍️ 🧐
• Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 🧐
• Single Cell / Scanpy Parameter Iterator 🧐
• Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) 📝 ⚙️ 🧐
• Using Galaxy and Managing your Data / Extracting Workflows from Histories 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐
• Imaging / Content Tracking and Verification in Galaxy Workflows with ISCC-SUM 🧐
• Epigenetics / DNA Methylation data analysis 📝
• Epigenetics / CUT&RUN data analysis ✍️ 🧐
• Epigenetics / Formation of the Super-Structures on the Inactive X ✍️ 🧐
• Proteomics / MaxQuant and MSstats for the analysis of label-free data 🧐
• Proteomics / Mass spectrometry imaging: Loading and exploring MSI data 🧐
• Proteomics / Single Cell Proteomics data analysis with bioconductor-scp 📝 🧐
• Proteomics / Metaproteomics tutorial 🧐
• Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🧐
• Introduction to Galaxy Analyses / Data Manipulation Olympics 🧐
• Introduction to Galaxy Analyses / Introduction to Galaxy as an RDM platform 🧐
• Transcriptomics / Genome-wide alternative splicing analysis 📝 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐
• Transcriptomics / RNA-RNA interactome data analysis ✍️
• Transcriptomics / Small Non-coding RNA Clustering using BlockClust ✍️ 🧐
• Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS 🧐
• Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package 🧐
• Metabolomics / Predicting EI+ mass spectra with QCxMS 🧐
• Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package 🧐
• Metabolomics / Mass spectrometry imaging: Finding differential analytes 🧐
• Metabolomics / Mass spectrometry: LC-MS analysis 🧐
• Metabolomics / Mass spectrometry: LC-MS data processing 🧐
• Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes 🧐
• Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) 🧐
• Statistics and machine learning / Unsupervised Analysis of Bone Marrow Cells with Flexynesis 🧐
• 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 🧑‍🏫

Your Contributor Card

GitHub Activity

github Issues Reported

63 Merged Pull Requests

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

• Correct marker gene assignments and rankings
  single-cell
• small changes to arabidopsis transcriptome analysis tutorial
  transcriptomics
• 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

Reviewed 48 PRs

We love our community reviewing each other's work!

• added tags required for metabolomics galaxy codex
  introduction
  proteomics
  metabolomics
  galaxy-interface
  computational-chemistry
• Montreal Forced Aligner tutorial
  template-and-tools
  digital-humanities
• Batch correction tutorial for single cell
  single-cell
• Adding tags
  single-cell
  CoFest_26
• Revise machine learning module description
  template-and-tools
  GTA

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