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.

• Single Cell
• Applying single-cell RNA-seq analysis
• Introduction to Galaxy and Single Cell RNA Sequence analysis
• Applying single-cell RNA-seq analysis in Coding Environments

Tutorials

• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝 🧐
• Single Cell / Inferring single cell trajectories with Scanpy 📝 🧐
• Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 📝 ⚙️ 🧐
• Single Cell / Pseudobulk Analysis with Decoupler and EdgeR 📝 🧐
• Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🧐
• Single Cell / Inferring single cell trajectories with Scanpy (Python) 🧐
• Single Cell / Combining single cell datasets after pre-processing 🧐
• 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 / Pre-processing of 10X Single-Cell ATAC-seq Datasets ✍️ 🧐
• Single Cell / Removing the effects of the cell cycle ⚙️
• Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝 🧐
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets ✍️ 🧐
• Single Cell / Single-cell quality control with scater ⚙️
• Single Cell / Generating a single cell matrix using Alevin 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) 🧐
• Single Cell / Importing files from public atlases 🧐
• Single Cell / Analysis of plant scRNA-Seq Data with Scanpy ✍️
• Single Cell / Clustering 3K PBMCs with Seurat 📝 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 🧐
• Single Cell / Converting between common single cell data formats ⚙️ 🧐
• Single Cell / Converting NCBI Data to the AnnData Format 📝 ⚙️ 🧐
• Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) 📝 ⚙️ 🧐
• Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution 🧐
• Proteomics / Single Cell Proteomics data analysis with bioconductor-scp 📝 🧐
• Proteomics / Metaproteomics tutorial 🧐
• Epigenetics / Formation of the Super-Structures on the Inactive X ✍️ 🧐
• Transcriptomics / Small Non-coding RNA Clustering using BlockClust ✍️ 🧐
• Transcriptomics / Genome-wide alternative splicing analysis 📝 🧐
• Transcriptomics / RNA-RNA interactome data analysis ✍️
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐
• Ecology / Production d'indicateurs champs de bloc 🧐

Slides

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

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 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

33 Merged Pull Requests

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

• add WF tests for scrna basic pipeline
  single-cell
• Add scrna-plant WF tests
  single-cell
• add workflow test for single-cell raceid tutorial
  single-cell
• Scanpy 3k PBMCs tutorial update history and workflow links
  single-cell
• correct the scanpy tool names in the tutorial
  single-cell

Reviewed 35 PRs

We love our community reviewing each other's work!

• Training for the bioconductor-scp tool
  template-and-tools
  proteomics
• Pseudobulk Analysis with Decoupler and edgeR
  single-cell
• Adding Seurat version of the PBMC clustering tutorial
  single-cell
• SPOC CoFest blog post
  news
• Update CoFest
  template-and-tools

News

External Links

Favourite Topics

Favourite Formats