Pavankumar Videm

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.

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

Tutorials

• Transcriptomics / Genome-wide alternative splicing analysis 📝 🧐
• Transcriptomics / Small Non-coding RNA Clustering using BlockClust ✍️ 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐
• Transcriptomics / RNA-RNA interactome data analysis ✍️
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Epigenetics / CUT&RUN data analysis ✍️ 🧐
• Epigenetics / Formation of the Super-Structures on the Inactive X ✍️ 🧐
• Epigenetics / DNA Methylation data analysis 📝
• Proteomics / Single Cell Proteomics data analysis with bioconductor-scp 📝 🧐
• Proteomics / Metaproteomics tutorial 🧐
• Single Cell / Generating a single cell matrix using Alevin 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 🧐
• 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 / Filter, plot, and explore single cell RNA-seq data with Seurat 📝 🧐
• Single Cell / Pseudobulk Analysis with Decoupler and EdgeR 📝 🧐
• Single Cell / Single-cell quality control with scater ⚙️
• Single Cell / Clustering 3K PBMCs with Scanpy ✍️ 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🖥 🧐
• Single Cell / Inferring single cell trajectories with Scanpy 📝 🧐
• Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝 🧐
• Single Cell / Inferring single cell trajectories with Scanpy (Python) 🧐
• Single Cell / Importing files from public atlases 🧐
• Single Cell / Combining single cell datasets after pre-processing 🧐
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝 🧐
• Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets ✍️ 🧐
• Single Cell / Converting NCBI Data to the AnnData Format 📝 ⚙️ 🧐
• Single Cell / Removing the effects of the cell cycle ⚙️
• Single Cell / Analysis of plant scRNA-Seq Data with Scanpy ✍️
• 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 Scanpy (Python) 🧐
• Single Cell / Downstream Single-cell RNA analysis with RaceID ⚙️
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets ✍️ 🧐
• Single Cell / Converting between common single cell data formats ⚙️ 🧐
• Single Cell / Clustering 3K PBMCs with Seurat 📝 🧐
• Ecology / Production d'indicateurs champs de bloc 🧐

Slides

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

Video Recordings

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

Events

• Workshop on high-throughput sequencing data analysis with 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 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

44 Merged Pull Requests

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

• [GTA] last couple of single-cell histories for GTA
  single-cell
  GTA
• Pseudobulk tutorial add histories from other servers
  single-cell
  GTA
• Add more single-cell histories
  single-cell
• Detailed program description of gta2025-single-cell track
  template-and-tools
  GTA
• Add more answer history links to single-cell tutorials
  single-cell

Reviewed 38 PRs

We love our community reviewing each other's work!

• Improve tutorial text for clarity of the video recording
  single-cell
• Update tutorial: Pseudobulk with decoupler and edgeR – Merge me for the GTA! 🚀
  single-cell
  GTA
• Update CUT and RUN tutorial
  epigenetics
• Training for the bioconductor-scp tool
  template-and-tools
  proteomics
• Pseudobulk Analysis with Decoupler and edgeR
  single-cell

News

External Links

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